Output with [X] symbol, wrong identification of data type

[Anna-pro]

Hello Patrick,
I have my protein alignments after Mafft in .fas format:

>WP_002656499.1
----------MSK-FFER------DDDIVALA-------TPFLSSALCVIRSS-------
----------GASSISKFSKI----FSNHSALNSASGNTIHYGYILDS------------
--------EN--------GCKVDEVVVCLYRAPKSFTGQDAIEVMAHGSVIGIKKIIDLF
LKSGFRMAEPGEFT--LRAFLAKKIDLTKAEAIHEIIFAKT-------------------
-------NKTYSLA-VNKLSGALFVKIDAIKKSILNFLSAVSVYLDYEVDD---------
---------------------HEISIPFDL----ILSSKAELKKLINSYKVYEKIDNGVA
LVLAGSVNAGKSSLFNLFLKKDRSIVSSYPGTTRDYIEASFELDGI-LFNLFDTAGLRD-
---------ADNFVERLGIEKSNSLIKEASLVIYVIDV-----SSNLTKD----DFLFID
S-------------------------------NKSNSKILFVLNKIDLK-----------
-------INKSTEEFV-------------------------------------RSKVLNS
SNLIMISTKNLEGIDILYDKIRALISYERVEIGL--------------------------
------------------------------------------------------------
-------DDIIIS-SNRQMQLLEKAYAL--------------------------------
ILDLLSK-----------IDR-QVSYD---------MLAFDAYEIIN-------------
------CLGEITGE---------VSSED------VLDNMFK-------------------
---NFCL--GK-

After running FASconCAT (perl FASconCAT-G_v1.04.pl -s -n -l) I received FcC_supermatrix.nex, which contains following:

#NEXUS

begin data;
dimensions ntax= 7893 nchar= 79315;
format datatype=dna interleave missing=-;
matrix
WP_013967880.1  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
WP_021687749.1  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
WP_002680262.1  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
disjointig_22_115  M------------------- -------------------- -------------------- -------------------- --------------------
WP_015712824.1  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
disjointig_54_381  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
disjointig_17_2181  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
disjointig_102_770  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
WP_044978940.1  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX
disjointig_31_1360  XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX XXXXXXXXXXXXXXXXXXXX

First question: why format data type identified as DNA? And probably it links to my next question:why sequences are mainly presented by [X] symbol?
I would appreciate any help and advices how I can fix it for further phylogenetic tree analysis. Thank you!

Best wishes,
Anna

[PatrickKueck]

#!/usr/bin/perl use strict; use File::Copy; use Tie::File; use Term::ANSIColor qw(:constants); use Getopt::Std; ######################################### ENTER THE PROTTEST SOFTWARE NAME OF YOUR RUNNING SYSTEM IN SINGLE QUOTATION MARKS '' # DEFINEMENT OF ACTUAL PROTTEST SOFTWARE NAME my $prottest = 'prottest-3.3.jar' ; ############################## # written by patrick k�ck, zentrales forschungsmuseum alexander koenig, bonn, germany # email: ***@***.*** # updated on 12th,january , 2009 by patrick kueck # updated on 25th may , 2009 by patrick kueck # updated on 28th may , 2009 by patrick kueck # updated on 7th june , 2009 by patrick kueck # updated on 8th june , 2009 by patrick kueck # updated on 28th september , 2009 by patrick kueck # updated on 16th october , 2009 by patrick kueck # updated on 17th november , 2009 by patrick kueck # updated on 7th january , 2010 by patrick kueck # updated on 7th april , 2010 by patrick kueck # updated on 8th april , 2010 by patrick kueck -> FcC v1.0 # updated on april , 2014 by patrick kueck -> FcC-G v1.0 # updated on 30th september , 2014 by patrick kueck -> FcC-G v1.01 Implementation of additional Screen Output (%Missing Data and Single Infile Sequence Ranges in the concatenated supermatrix) as well as some output result file format changes # updated on 16th november , 2014 by patrick kueck ->input file endings line 1529-1531->FcC v1.03 # updated on 22nd november , 2016 by patrick kueck -> concatenation and print out of supermatrix ranges due to sorted infile names and not randomly. Debuged read in error of .FASTA or .fasta named files # updated on 22nd march , 2021 by patrick kueck -> FcC-G v1.05 Including an additional character coding option for absent sequence data (-g). With -g, absent sequence data is filled by '-' rather than 'N/X' during the concatenation process # updated on 22nd february , 2022 by jgl -> FcC-G v1.05.1 Resolved command conflict: 'Replace missing sequences with' set to (-g); 'Preface' set to (-x); some minor character corrections to comments # updated on 19th april , 2022 by patrick kueck -> FcC-G_v1.05.2 Resolved empty line conflict at the end of phylip files (last sequence followed by multiple newlines) in &phy2fas ####################################################### START ####################################################################################### my %outfile_name = ( 'supermatrixFAS' => 'FcC_smatrix.fas', # Supermatrix outfile in FASTA format 'supermatrixPHY' => 'FcC_smatrix.phy', # Supermatrix outfile in PHYLIP format 'supermatrixNEX' => 'FcC_smatrix.nex', # Supermatrix outfile in NEXUS format 'structure' => 'FcC_structure.txt', # Structure sequence info file 'info' => 'FcC_info.xls', # Sequence states & concatenation info file 'prottest' => $prottest, # Name of defined prottestversion ) ; my @parameter_all = ( 'YES', 'NO' ) ; # Parameter option of data concatenation -> 'YES' -> concatenate all files; 'NO' -> concatenate defined files my @parameter_info = ( 'YES', 'NO' ) ; # Parameter option of additional sequence state analysis -> 'YES' -> perform and print ; 'NO' -> print only basal sequence info my @parameter_tra = ( 'NO', 'NUC to AA','AA to NUC' ) ; # Parameter option of sequence transaltion -> 'NUC to AA' -> translate nucleotide data to amino acid data; 'AA to NUC' -> translate amino acid data to nucleotide data my @parameter_phy = ( 'NO', 'STRICT', 'RELAXED' ) ; # Print supermatrix in PHYLIP format my @parameter_nex = ( 'NO', 'BLOCK', 'MrBAYES' ) ; # Print supermatrix in NEXUS format my @parameter_fas = ( 'YES', 'NO' ) ; # Print supermatrix in FASTA format my @parameter_con = ( 'NO', 'Freq', 'Maj', 'Strict' ) ; # Perform consensus sequence of defined sequence blocks my @parameter_file = ( 'Supermatrix', 'Convert', 'Supermatrix/Convert' ) ; # Concatenate, Convert, or both define by associated option -> 'Supermatrix': concatenation; Convert: Converting single files without adding missing sequences; 'Supermatrix/Convert': Concatenated single files and convert single files with included missing sequence taxa my @parameter_3rd = ( 'Remain', 'Reject' ) ; # Parameter option of 3rd sequence position exclusion -> 'Remain' -> remove third position; 'Reject' -> keep third position my @parameter_ryc = ( 'NO', 'All', '3rd' ) ; # Parameter option of RY coding -> 'NO' -> no RY coding; 'All' -> RY coding of complete sequence; '3rd' -> RY coding of 3rd sequence positions my @parameter_par = ( 'NO', 'YES' ) ; # Print parsimonious sites as extra msa file -> 'NO' -> no print; 'YES' -> print my @parameter_ren = ( 'NO', 'YES' ) ; # Rename taxon names of given infiles -> 'NO' ; 'YES' my @parameter_prt = ( 'NO', 'Supermatrix' ) ; # Print OUT additional partition files if concatenated -> 'NO' ; 'Supermatrix' means yes for concatenatde files my @parameter_pro = ( 'NO', 'Supermatrix' ) ; # Start prottest analyses for aa data -> 'NO' ; 'YES' my @parameter_mis = ( 'Missing', 'Indel' ) ; # Replace missing sequences with -> 'Missing': 'X' or 'N' ; 'Indel': '-' ############################## ## READ IN ARGV and assign user defined parameter options &argv_handling ( ***@***.***_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) ***@***.***_info, # List of parameter options of info print out -> IN (defined) / OUT (changed) ***@***.***_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) ***@***.***_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) ***@***.***_con, # List of consensus options -> IN (defined) / OUT (changed) ***@***.***_file, # List of filehandling options -> IN (defined) / OUT (changed) ***@***.***_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) ***@***.***_3rd, # List of third position handling -> IN (defined) / OUT (changed) ***@***.***_ryc, # List of RY coding -> IN (defined) / OUT (changed) ***@***.***_tra, # List of Sequence transaltion options -> IN (defined) / OUT (changed) ***@***.***_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) ***@***.***_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) ***@***.***_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) ***@***.***_pro, # Start prottest analyses for aa data -> IN (defined) / OUT (changed) ***@***.***_mis, # Replace missing gene sequences by '-' instead using 'X' or 'N' -> IN (defined) / OUT (changed) \%outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ) ; ############################## ############################## ## Open MENU &menu ; ############################## ############################## ## Open Parameter setup &parameter( ***@***.***_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) ***@***.***_info, # List of parameter options of info print out -> IN (defined) / OUT (changed) ***@***.***_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) ***@***.***_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) ***@***.***_con, # List of consensus options -> IN (defined) / OUT (changed) ***@***.***_file, # List of filehandling options -> IN (defined) / OUT (changed) ***@***.***_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) ***@***.***_3rd, # List of third position handling -> IN (defined) / OUT (changed) ***@***.***_ryc, # List of RY coding -> IN (defined) / OUT (changed) ***@***.***_tra, # List of Sequence transaltion options -> IN (defined) / OUT (changed) ***@***.***_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) ***@***.***_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) ***@***.***_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) ***@***.***_pro, # Start prottest analyses for aa data -> IN (defined) / OUT (changed) ***@***.***_mis, # Replace missing gene sequences by '-' instead using 'X' or 'N' -> IN (defined) / OUT (changed) \%outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ); ############################## ################################################################## END ############################################################################### sub argv_handling{ my $aref_parameter_all = $_[0] ; # List of parameter options of data concatenation -> IN (defined) / OUT (changed) my $aref_parameter_inf = $_[1] ; # List of parameter options of info print out -> IN (defined) / OUT (changed) my $aref_parameter_phy = $_[2] ; # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) my $aref_parameter_nex = $_[3] ; # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) my $aref_parameter_con = $_[4] ; # List of consensus options -> IN (defined) / OUT (changed) my $aref_parameter_fil = $_[5] ; # List of of file handling -> IN (defined) / OUT (changed) my $aref_parameter_fas = $_[6] ; # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) my $aref_parameter_3rd = $_[7] ; # List of third position handling -> IN (defined) / OUT (changed) my $aref_parameter_ryc = $_[8] ; # List of RY coding -> IN (defined) / OUT (changed) my $aref_parameter_tra = $_[9] ; # List of sequence translation options -> IN (defined) / OUT (changed) my $aref_parameter_par = $_[10]; # List of sequence translation options -> IN (defined) / OUT (changed) my $aref_parameter_ren = $_[11]; # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) my $aref_parameter_prt = $_[12]; # Print partition files for concatenated data -> IN (defined) / OUT (changed) my $aref_parameter_pro = $_[13]; # Start prottest analyses for aa data -> IN (defined) / OUT (changed) my $aref_parameter_mis = $_[14]; # Replace missing gene sequences by '-' instead using 'X' or 'N' -> IN (defined) / OUT (changed) my $href_outfile_name = $_[15]; # Outfilename of output option -> IN (defined) / OUT (unchanged) ############################## START ARGV READ IN ## READ IN and assign terminal command options ## Set chosen parameter option one step further if associated command option is given my ( $commandline ) = join "", @argv ; if ( $commandline ){ ############################## ## substitute blanks to '' & split up commandline using '-' signs ## delete first (empty) entry in @commands $commandline =~ s/ |\s+// ; my @commands = split '-', $commandline ; shift @commands; ############################## ############################## ## Change parameter of given command ## Skip to main menu if a command option is unknown ## or '-s' command missing for my $single_command ( sort @commands ){ if ( $single_command =~ /^help$/i ) { &help } # '-help' -> open help menu elsif ( $single_command =~ /^i$/i ) { @$aref_parameter_inf = reverse @$aref_parameter_inf } # '-i' -> set additional info print to NO; '-i -i' -> to NO elsif ( $single_command =~ /^f$/i ) { @$aref_parameter_all = reverse @$aref_parameter_all } # '-f' -> set infile READ IN to defined; '-f -f' -> to all possible infiles elsif ( $single_command =~ /^a$/i ) { @$aref_parameter_fas = reverse @$aref_parameter_fas } # '-a' -> set FASTA output to NO; '-a -a' -> to YES elsif ( $single_command =~ /^d$/i ) { @$aref_parameter_3rd = reverse @$aref_parameter_3rd } # '-d' -> Reject 3rd position; '-d -d' -> Remain 3rd position elsif ( $single_command =~ /^j$/i ) { @$aref_parameter_par = reverse @$aref_parameter_par } # '-j' -> set PARSIMONY output to YES; '-j -j' -> to NO elsif ( $single_command =~ /^k$/i ) { @$aref_parameter_ren = reverse @$aref_parameter_ren } # '-k' -> set rename of sequence names to YES; '-k -k' -> to NO elsif ( $single_command =~ /^l$/i ) { @$aref_parameter_prt = reverse @$aref_parameter_prt } # '-l' -> set part. file of conc matrix to Supermatrix; '-l -l' -> to NO elsif ( $single_command =~ /^m$/i ) { @$aref_parameter_pro = reverse @$aref_parameter_pro } # '-m' -> start prottest under linux; '-m -m' -> don't start prottest (default) elsif ( $single_command =~ /^g$/i ) { @$aref_parameter_mis = reverse @$aref_parameter_mis } # '-g' -> replace missing sequences by '-'; '-g -g' -> replace missing sequences by 'X' or 'N' (default) #jgl#'-x -> -g'#jgl# elsif ( $single_command =~ /^e$/i ) { my $tl = shift @$aref_parameter_tra ; push @$aref_parameter_tra, $tl } # '-e' -> translate nuc data to aa data; '-e -e' -> translate aa data to nuc data '-e -e -e' -> no translation elsif ( $single_command =~ /^c$/i ) { my $tl = shift @$aref_parameter_con ; push @$aref_parameter_con, $tl } # '-c' -> Generate frequency consensus sequence; '-c -c' -> majority consensus; '-c -c -c' -> strict consensus; '-c -c -c -c' -> to default (no consensus) elsif ( $single_command =~ /^p$/i ) { my $tl = shift @$aref_parameter_phy ; push @$aref_parameter_phy, $tl } # '-p' -> set supermatrix format to strict phylip; '-p -p' -> to relaxed phylip; '-p -p -p' -> to default (no phylip) elsif ( $single_command =~ /^n$/i ) { my $tl = shift @$aref_parameter_nex ; push @$aref_parameter_nex, $tl } # '-n' -> set supermatrix format to nexus block; '-n -n' -> to MrBayes nexus block; '-n -n -n' -> to default (no nexus) elsif ( $single_command =~ /^o$/i ) { my $tl = shift @$aref_parameter_fil ; push @$aref_parameter_fil, $tl } # '-o' -> convert only infiles; '-o -o' -> Supermatrix & infiles; '-o -o -o' -> print out only supermatrix file elsif ( $single_command =~ /^b$/i ) { my $tl = shift @$aref_parameter_ryc ; push @$aref_parameter_ryc, $tl } # '-b' -> RY coding complete sequences '-b -b' -> RY coding 3rd positions; '-b -b -b' -> no RY coding elsif ( $single_command =~ /^s$/i ) { # '-s' -> Start FASconCAT &start( \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (changed) \@$aref_parameter_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (changed) \@$aref_parameter_fil, # List of of file handling -> IN (defined) / OUT (changed) \@$aref_parameter_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (changed) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (changed) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (changed) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) \@$aref_parameter_pro, # Start Prottest -> IN (defined) / OUT (changed) \@$aref_parameter_mis, # Replacement code of missing sequences -> IN (defined) / OUT (changed) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ) } else { print "\n\tCOMMAND-ERROR!: Unknown command ", $single_command, "!\n" ; # 'unknown command' -> print ERROR prompt ############################## ## Open Menu if unknown command is given &menu ; &parameter ( \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (changed) \@$aref_parameter_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (changed) \@$aref_parameter_fil, # List of of file handling -> IN (defined) / OUT (changed) \@$aref_parameter_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (changed) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (changed) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (changed) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) \@$aref_parameter_pro, # Start Prottest -> IN (defined) / OUT (changed) \@$aref_parameter_mis, # Replacement code of missing sequences -> IN (defined) / OUT (changed) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ) ############################## } } ############################## ## Open Menu if '-s' command is missing &menu ; &parameter ( \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (changed) \@$aref_parameter_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (changed) \@$aref_parameter_fil, # List of of file handling -> IN (defined) / OUT (changed) \@$aref_parameter_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (changed) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (changed) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (changed) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) \@$aref_parameter_pro, # Start Prottest -> IN (defined) / OUT (changed) \@$aref_parameter_mis, # Replacement code of missing sequences -> IN (defined) / OUT (changed) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ) ############################## } ############################## END ARGV READ IN } sub menu{ system('cls'); print ""; printf "\n%68s\n","------------------------------------------------------------" ; printf "%53s\n" , "Welcome to FASconCAT-G v1.0 !" ; printf "%58s\n" , "A perlscript for sequence concatenation" ; printf "%59s\n" , "written by Patrick Kueck (ZFMK Bonn, 2010/14)" ; printf "%68s\n\n", "------------------------------------------------------------" ; } sub parameter{ my $aref_parameter_all = $_[0] ; # List of parameter options of data concatenation -> IN (defined) / OUT (changed) my $aref_parameter_inf = $_[1] ; # List of parameter options of info print out -> IN (defined) / OUT (changed) my $aref_parameter_phy = $_[2] ; # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) my $aref_parameter_nex = $_[3] ; # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) my $aref_parameter_con = $_[4] ; # List of consensus options -> IN (defined) / OUT (changed) my $aref_parameter_fil = $_[5] ; # List of of file handling -> IN (defined) / OUT (changed) my $aref_parameter_fas = $_[6] ; # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) my $aref_parameter_3rd = $_[7] ; # List of third position handling -> IN (defined) / OUT (changed) my $aref_parameter_ryc = $_[8] ; # List of RY coding -> IN (defined) / OUT (changed) my $aref_parameter_tra = $_[9] ; # List of sequence translation options -> IN (defined) / OUT (changed) my $aref_parameter_par = $_[10]; # List of sequence translation options -> IN (defined) / OUT (changed) my $aref_parameter_ren = $_[11]; # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) my $aref_parameter_prt = $_[12]; # Print partition files for concatenated data -> IN (defined) / OUT (changed) my $aref_parameter_pro = $_[13]; # Start prottest analyses f�r aa data -> IN (defined) / OUT (changed) my $aref_parameter_mis = $_[14]; # Replacement code of missing gene sequences -> IN (defined) / OUT (changed) my $href_outfile_name = $_[15]; # Outfilename of output option -> IN (defined) / OUT (unchanged) ############################## ## Print parameter setting and available command options print "\tSTART\t FASconCAT :\t\t type <s> <enter>", "\n", "\n\tINFILES\t ALL/SINGLE :\t\t type <f> <enter>", "\n\tINFO\t ALL/BASIC :\t\t type <i> <enter>", "\n", "\n\tPROCESSING SMATRIX/CONV. :\t\t type <o> <enter>", "\n\tSEQ.TRANS. NO/NUC/AA :\t\t type <e> <enter>", "\n\t3rd POS. REMAIN/REJECT :\t\t type <d> <enter>", "\n\tRY CODING NO/ALL/3rd :\t\t type <b> <enter>", "\n\tCONSENSUS N0/YES :\t\t type <c> <enter>", "\n\tRENAME SEQ NO/YES :\t\t type <k> <enter>", "\n\tABSENT SEQ MISSING/INDEL :\t\t type <g> <enter>", "\n", "\n\tNEXUS BLOCK/MrBAYES :\t\t type <n> <enter>", "\n\tPHYLIP NO/YES :\t\t type <p> <enter>", "\n\tFASTA YES/NO :\t\t type <a> <enter>", "\n\tPARTITION NO/Supermatrix:\t\t type <l> <enter>", "\n\tPARSIMONY NO/YES :\t\t type <j> <enter>", "\n\tPROTTEST NO/YES :\t\t type <m> <enter>", "\n", "\n\tHELP FASconCAT :\t\t type <h> <enter>", "\n\tQUIT FASconCAT :\t\t type <q> <enter>", "\n\tPREFACE FASconCAT :\t\t type <x> <enter>", #jgl#'<g> -> <x>'#jgl# "\n", "\n\t------------------------------------------------------------", "\n", "\n\tFILE INPUT", "\n\t-----------------", "\n\tPROCESSING ALL FILES :\t$aref_parameter_all->[0]", "\n\tPROCESSING SINGLE FILES :\t$aref_parameter_all->[1]", "\n\tPROCESSING SEQ. TRANSL. :\t$aref_parameter_tra->[0]", "\n\tPROCESSING 3rd POSITION\t :\t$aref_parameter_3rd->[0]", "\n\tPROCESSING RY CODING\t :\t$aref_parameter_ryc->[0]", "\n\tPROCESSING CONSENSUS\t :\t$aref_parameter_con->[0]", "\n\tRENAME SEQUENCE NAMES\t :\t$aref_parameter_ren->[0]", "\n\tREPLACE ABSENT SEQUENCE\t :\t$aref_parameter_mis->[0]", "\n", "\n\tFILE OUTPUT", "\n\t-----------------", "\n\tALL INFO :\t$aref_parameter_inf->[0]", "\n\tFILE PROCESSING :\t$aref_parameter_fil->[0]", "\n\n\tNEXUS :\t$aref_parameter_nex->[0]", "\n\tPHYLIP :\t$aref_parameter_phy->[0]", "\n\tFASTA :\t$aref_parameter_fas->[0]\n", "\n\tPARTITION FILE :\t$aref_parameter_prt->[0]", "\n\tPARSIMONY :\t$aref_parameter_par->[0]", "\n\tPROTTEST :\t$aref_parameter_pro->[0]\n", "\n\t------------------------------------------------------------" ; ############################## ############################## ## (1) Read IN user defined command #jgl#'=> d'#jgl# ## (2) If command option allowed, change parameter setting ## (3) unless user defined command allowed print error prompt my $start_string ; my $single_command = &commandline ( \$start_string ) ; # (1) # (2) unless ( $single_command =~ /^s$|^i$|^f$|^q$|^h$|^n$|^p$|^a$|^c$|^o$|^a$|^b$|^q$|^d$|^e$|^g$|^j$|^k$|^l$|^g$|^m$|^x$/i ){ print "\n\tCOMMAND-ERROR!: Unknown command ".$single_command."!\n" } #jgl#'=> $|^x'#jgl# # (3) if ( $single_command =~ /^h$/i ) { &help } # '-h' -> open help menu elsif ( $single_command =~ /^x$/i ) { &preface} # '-x' -> open preface menu #jgl#'/^g> -> /^x' ; '-e -> -x'#jgl# elsif ( $single_command =~ /^q$/i ) { exit } # '-q' -> exit FASconCAT elsif ( $single_command =~ /^i$/i ) { @$aref_parameter_inf = reverse @$aref_parameter_inf } # '-i' -> set additional info print to YES; '-i -i' -> to NO elsif ( $single_command =~ /^f$/i ) { @$aref_parameter_all = reverse @$aref_parameter_all } # '-f' -> set infile READ IN to defined; '-f -f' -> to all possible infiles elsif ( $single_command =~ /^a$/i ) { @$aref_parameter_fas = reverse @$aref_parameter_fas } # '-a' -> set FASTA output to NO; '-a -a' -> to YES elsif ( $single_command =~ /^j$/i ) { @$aref_parameter_par = reverse @$aref_parameter_par } # '-j' -> set PARSIMONY output to YES; '-j -j' -> to NO elsif ( $single_command =~ /^d$/i ) { @$aref_parameter_3rd = reverse @$aref_parameter_3rd } # '-d' -> Reject 3rd position; '-d -d' -> Remain 3rd position elsif ( $single_command =~ /^k$/i ) { @$aref_parameter_ren = reverse @$aref_parameter_ren } # '-k' -> set rename of sequence names to YES; '-k -k' -> to NO elsif ( $single_command =~ /^l$/i ) { @$aref_parameter_prt = reverse @$aref_parameter_prt } # '-l' -> set part. file of conc matrix to Supermatrix; '-l -l' -> to NO elsif ( $single_command =~ /^m$/i ) { @$aref_parameter_pro = reverse @$aref_parameter_pro } # '-m' -> start prottest under linux; '-m -m' -> don't start prottest (default) elsif ( $single_command =~ /^g$/i ) { @$aref_parameter_mis = reverse @$aref_parameter_mis } # '-g' -> replace missing sequences by '-'; '-g -g' -> replace missing sequences by 'X' or 'N' (default) #jgl#'-x -> -g'#jgl# elsif ( $single_command =~ /^e$/i ) { my $tl = shift @$aref_parameter_tra ; push @$aref_parameter_tra, $tl } # '-e' -> translate nuc data to aa data; '-e -e' -> translate aa data to nuc data '-e -e -e' -> no translation elsif ( $single_command =~ /^c$/i ) { my $tl = shift @$aref_parameter_con ; push @$aref_parameter_con, $tl } # '-c' -> Generate frequency consensus sequence; '-c -c' -> majority consensus; '-c -c -c' -> strict consensus; '-c -c -c -c' -> to default (no consensus) elsif ( $single_command =~ /^p$/i ) { my $tl = shift @$aref_parameter_phy ; push @$aref_parameter_phy, $tl } # '-p' -> set supermatrix format to strict phylip; '-p -p' -> to relaxed phylip; '-p -p -p' -> to default (no phylip) elsif ( $single_command =~ /^n$/i ) { my $tl = shift @$aref_parameter_nex ; push @$aref_parameter_nex, $tl } # '-n' -> set supermatrix format to nexus block; '-n -n' -> to MrBayes nexus block; '-n -n -n' -> to default (no nexus) elsif ( $single_command =~ /^b$/i ) { my $tl = shift @$aref_parameter_ryc ; push @$aref_parameter_ryc, $tl } # '-b' -> RY coding complete sequences '-b -b' -> RY coding 3rd positions; '-b -b -b' -> no RY coding elsif ( $single_command =~ /^o$/i ) { my $tl = shift @$aref_parameter_fil ; push @$aref_parameter_fil, $tl } # '-o' -> convert only infiles; '-o -o' -> Supermatrix & infiles; '-o -o -o' -> print out only supermatrix file elsif ( $single_command =~ /^s$/i ) { # '-s' -> Start FASconCAT &start( \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (changed) \@$aref_parameter_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (changed) \@$aref_parameter_fil, # List of of file handling -> IN (defined) / OUT (changed) \@$aref_parameter_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (changed) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (changed) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (changed) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) \@$aref_parameter_pro, # Start Prottest -> IN (defined) / OUT (changed) \@$aref_parameter_mis, # Replacement code of missing gene sequences -> IN (defined) / OUT (changed) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ) } &menu; &parameter( \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (changed) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (changed) \@$aref_parameter_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (changed) \@$aref_parameter_fil, # List of of file handling -> IN (defined) / OUT (changed) \@$aref_parameter_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (changed) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (changed) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (changed) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (changed) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (changed) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (changed) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (changed) \@$aref_parameter_pro, # Start Prottest -> IN (defined) / OUT (changed) \@$aref_parameter_mis, # Replacement code of missing gene sequences -> IN (defined) / OUT (changed) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ) ; ############################## } sub help{ system('cls'); print <<help

…

--------------------FASconCAT-G HELP-MENU--------------------------- 'Features' -------------------------- - Sequence concatenation of single infiles of different formats: - FASTA (.fas or .FASTA) - PHYLIP (.phy -> Relaxed or Strict) - CLUSTAL (.aln) - Individual character fill of absent gene sequences (either by missing chars 'X'|'N' or indels '-') - Multiple supermatrix output formats in one process run: - FASTA (.fas or .FASTA) - PHYLIP (.phy -> Relaxed or Strict) - NEXUS (.nex -> BLOCK with or without MrBayes commands) - Multiple file conversion of infiles in one process run: - FASTA (.fas or .FASTA) - PHYLIP (.phy -> Relaxed or Strict) - NEXUS (.nex -> BLOCK with or without MrBayes commands) - Processing of specific consensus sequences using either... - Strict consensus rules - Majority consensus rules or - Frequency consensus rules - RY-Coding of complete sequences (nucleotide data only) - RY-Coding of 3rd codon positions (nucleotide data only) - Removing of 3rd codon positions (nucleotide data only) - Sequence translation (nucleotide data to amino acid data and vice versa) - Print OUT of parsimony informative sites within infiles and concatenated supermatrix - Handling & identification of specific secondary structure positions - Additional output information includes... - Infile ranges in supermatrix sequences - Character state distributions within individual infiles and the supermatrix - Sequence type of individual infiles and the supermatrix - Sequence lengths of individual infiles - Number of gaps and ambiguous sites within infiles and the supermatrix - Number of missing sequences for each individual from the supermatrix - Number of GC character states within individual infiles and the supermatrix - Number of parsimony informative sites in individual infiles and the supermatrix - Proportion of character states in supermatrix sequences - Proportion of gaps and ambiguous sites in supermatrix sequences - Proportion of GC in supermatrix sequences - Proportion of parsimony informative sites in supermatrix sequences - Number of structure characters seperated in loops and stems - Number and percent of loop and stem positions per fragment - Separated list (FcC_structure.txt) for loop positions and stem pairings whitin the supermatrix and the infiles - All features can be optionally combined or modified via: - Terminal command line - The FASconCAT (FcC) terminal menu -------------------------- 'Start FASconCAT' -------------------------- To start FASconCAT, open the script by via the terminal. Via FASconCAT terminal menu: - Open the menu by entering command: perl FASconCAT-G_v1.0.pl <enter> (Linux/Mac) FASconCAT-G_v1.0.pl <enter> (Windows) - To start FASconCAT under default, enter command: s <enter> Via terminal command line, enter command: - perl FASconCAT_v1.0.pl [command options] <enter> (Linux/Mac) - FASconCAT_v1.0.pl [command options] <enter> (Windows) - To start FASconCAT under default, enter command: perl FASconCAT_v1.0.pl -s <enter> -------------------------- Command options: -------------------------- The following command options can be used as stand alone commands or in combination with other commands. Command options can be invoked in a single line via the terminal command window or individually via the FASconCAT menu (without the minus'-' specification in the menu). Command options can be input in any order. - Output processing (-o option) - FcC can be used for sequence concatenation and/or file conversion. - Under default, FcC prints OUT a supermatrix with concatenated sequences in FASTA format in a file called "FcC_supermatrix.fas". - For infile format conversions WITHOUT printing a supermatrix, enter command: -o - For format conversions of given infiles AND concatenated supermatrix output, enter command: -o -o - Sequence translation (-e option) - FcC can translate nucleotide data to amino acid data and vice versa. Sequence translation happens before exclusion of third nucleotide codon positions (if -d option is defined). - FcC does not recognize stop codons in amino acid data or reading frames in nucleotide data. Stop codons have to be excluded in amino acid data before using FcC! - Nucleotide triplets are translated to their corresponding amino acid. Ambiguity states in triplets are recognized if their coding nucleotide states can be definitively assigned to a specific amino acid state (e.g., 'YTR' -> Leucine/L). Undefined triplets, such as 'A-G' are translated to '?'. To select for translation of nucleotide data, enter command: -e - Amino acid states are translated to nucleotide triplets using the compressed IUPAC triplet code for the corresponding amino acid (e.g. Phenylalanin/F -> 'TTY'). Unrecognized states, such as '-' or 'X', are translated to '???'. To define reverse translation of amino acid data, enter command: -e -e - Character fill of lacking gene sequences (-g option) - Under default, lacking sequences in single genes are filled by 'X' (amino-acid) or 'N' (nucleotide): 'MISSING'. With the -g command, lacking sequences are filled by indel characters '-' instead of missing sequence code: 'INDEL' - Renaming sequence names (-k option) - To rename defined sequence names prior to file file processing, enter command: -k - Note: the user must provide an extra info file named "new_seq_names.txt" in the FcC home folder where each row has the old name delimited from the new name by a tabstop. - Sequences not specified in the "new_seq_names.txt" file are left unchanged. FcC prints additional information of the renaming process to "FcC_rename_control.txt". - Rejecting 3rd codon position (-d option) - To exclude 3rd codon positions in given nucleotide infiles and/or supermatrices, enter command: -d - RY coding (-b option) - To translate third codon positions of nucleotide data into R/Y code (nucleotide data only), enter command: -b e.g., File_1 (nucleotide data): tax1_allel_0 ACGTTTTGGTTT -> ACRTTYTGRTTY... - To translate complete sequences into R/Y code, enter command: -b -b e.g., File_1 (nucleotide data): tax1_allel_0 ACGTTTTGGTTT -> RYRYYYYRRYYY... - Processing consensus sequences (-c option) - FASconCAT can generate consensus sequences for given infile and/or supermatrix sequences by building consensus states for sequences with identical sequence names (identical alphanumeric characters before the first underscore). Consensus outfile sequences are named by their sequence names, followed by the suffix '_consensus'. If no underscore is found in sequence names, FcC will use the complete sequence name for identification of unique sequences. e.g., MSA infile: -> Consensus outfile: Taxon_1 AAAACCC Taxon_2 AAAACCC Taxon AAAACCC -> Taxon_consensus AAAACCC taxon1 AAAACCC -> taxon_1_consensus AAAACCC Tax_1 AAAGCCT Tax_2 AAAGCCT -> Tax_consensus AAAGCCT - There are three different options for building a consensus sequence: - Most frequent, enter command: -c - Majority rule, enter command: -c -c - Strict, enter command: -c -c -c - Most Frequent ('Freq') - Builds consensus by taking most frequent character state of each site. If two or more character states are equally frequent, FASconCAT uses the corresponding IUPAC ambiguity code as the consensus state for nucleotide data or '?' (amino acid data). e.g., File_1 (nucleotide data): tax1_allel_0 ACGTTTTCGTTT... tax1_allel_1 ACGTTTTGTTTT... tax1_allel_2 ACGTTTTGGTTT... tax1 ACGTTTTTTTTT... -------------- tax1_consensus ACGTTTTGKTTT... e.g., File_2 (amino acid data): tax1_allel_0 NYGKRDEDPWFP... tax1_allel_1 NYGKRDEDCWFP... tax1_allel_2 NYGKRDEQCWFP... tax1 NYGKRDEQCWFP... -------------- tax1_consensus NYGKRDE?CWFP... - Majority Frequent ('Maj'): - Builds consensus by only considering character states that occur in more than 50% of sequences on a specific site as consensus state, otherwise assigns '?' (nucleotide & amino acid data). e.g., File_1 (nucleotide or amino acid data): tax1_allel_0 ACGTTTTGGTTT... tax1_allel_1 ACGTTTTGTTTT... tax1_allel_2 ACGTTTTGGTTT... tax1 ACGTTTTTTTTT... -------------- tax1_consensus ACGTTTTG?TTT... - Strict Consensus ('Strict'): - Builds consensus by taking either sequence states which are fixed in all sequences at a given site or by using the corresponding IUPAC ambiguity code (nucleotide data) or 'X' (amino acid data) e.g., File_1 (nucleotide data): tax1_allel_0 ACGTTTTGGTTT... tax1_allel_1 ACGTTTTGTTTT... tax1_allel_2 ACGTTTTGGTTT... tax1 ACGTTTTTTTTT... -------------- tax1_consensus ACGTTTTKKTTT... e.g., File_2 (amino acid data): tax1_allel_0 NYGKRDEDPWFP... tax1_allel_1 NYGKRDEDCWFP... tax1_allel_2 NYGKRDEQCWFP... tax1 NYGKRDEQCWFP... -------------- tax1_consensus NYGKRDEXXWFP... - READ IN specific sequence infiles (-f option) - Under default settings, FASconCAT reads in all files in the working directory that are in FASTA (.fas or .FASTA), PHYLIP (.phy) or CLUSTAL (.aln) format. If the '-f' option is chosen, a new list-window opens after starting FcC. Here input files can be defined by typing each files assigned numbers (separated by commas and without line spaces) in a single row. e.g. -f -s <enter> : 0 infile_1.fas 1 infile_2.phy 2 infile_3.aln 3 infile_4.FASTA Type: 1,2 <enter> to choose infile_2.phy & infile_3.aln - Reduction of FASconCAT sequence information (-i option) - To increase computation speed and reduce the amount of information FcC prints OUT regarding the infiles and supermatrix, enter command: -i - Print OUT of parsimony informative sites (-j option) - FASconCAT can print OUT parsimony informative sites for given infiles and the supermatrix (regarded to the selected -o option). To print OUT parsimony informative sites, enter command: -j - Definition of output file formats: - Under default options, FASconCAT prints all output files in FASTA format. To switch off output of FASTA formatted files, enter command: -a - FcC can also output NEXUS and PHYLIP formatted files: - To output files in PHYLIP (STRICT) format (sequence names are restricted to 10 characters), enter command: -p - To output files in PHYLIP (RELAXED) format (sequence names can be up to 250 characters), enter command: -p -p - To output files in NEXUS (BLOCK) format (NEXUS blocks), enter command: -n - To output files in NEXUS (MrBAYES) format (NEXUS blocks with additional MrBayes commands), enter command: -n -n - Print OUT partition file(s) (-l option) - When the sequence concatenation option has been defined, the user can print additional partition files by entering this command: -l - If the user selects to output a supermatrix in FASTA and/or PHYLIP format, FcC will print an associated gene partition file "FcC_supermatrix_partition.txt", which can be directly used for maximum likelihood analyses in RAxML. - If the user has selected to output a supermatrix in NEXUS (MrBayes) format, FcC prints an additional NEXUS file "FcC_supermatrix_partition.nex" in which gene partitions are defined. - Note: the parameters in the partitioned NEXUS (MrBayes) file differ from those in the non-partitioned version.

-------------------------- For further detailed information please consult the manual or write an email to ***@***.*** ------------------------------------------------------------ help ; print "\tBACK to FASconCAT MAIN-Menu:\t\t type <return>\n" ; print "\n\t------------------------------------------------------------\n\t" ; chomp ( my $answer_xy = <STDIN> ); &menu; &parameter ; } sub preface{ system('cls'); print <<preface

--------------------FASconCAT PREFACE--------------------- Version : G-1.0 Language : PERL Last Update : March, 2021 Author : Patrick Kueck, ZFMK Bonn, GERMANY e-mail : ***@***.*** Homepage : https://github.com/PatrickKueck/FASconCAT-G This program is free software; you can distribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation ; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA. For further free downloadable programs visit: http://software.zfmk.de

------------------------------------------------------------ preface ; print "\tBACK to FASconCAT MAIN-Menu:\t\t type <return>\n" ; print "\n\t------------------------------------------------------------\n\t" ; chomp ( my $answer_xy = <STDIN> ); &menu; &parameter ; } sub start{ my $aref_parameter_all = $_[0] ; # List of parameter options of data concatenation -> IN (defined) / OUT (unchanged) my $aref_parameter_inf = $_[1] ; # List of parameter options of info print out -> IN (defined) / OUT (unchanged) my $aref_parameter_phy = $_[2] ; # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (unchanged) my $aref_parameter_nex = $_[3] ; # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (unchanged) my $aref_parameter_con = $_[4] ; # List of consensus options -> IN (defined) / OUT (unchanged) my $aref_parameter_fil = $_[5] ; # List of of file handling -> IN (defined) / OUT (unchanged) my $aref_parameter_fas = $_[6] ; # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (unchanged) my $aref_parameter_3rd = $_[7] ; # List of third position handling -> IN (defined) / OUT (unchanged) my $aref_parameter_ryc = $_[8] ; # List of RY coding -> IN (defined) / OUT (unchanged) my $aref_parameter_tra = $_[9] ; # List of sequence translation options -> IN (defined) / OUT (unchanged) my $aref_parameter_par = $_[10]; # Print parsimonious sites as extra msa file -> IN (defined) / OUT (unchanged) my $aref_parameter_ren = $_[11]; # Rename taxon names of given ifiles -> IN (defined) / OUT (unchanged) my $aref_parameter_prt = $_[12]; # Print partition files for concatenated data -> IN (defined) / OUT (unchanged) my $aref_parameter_pro = $_[13]; # Start prottest analyses for aa data -> IN (defined) / OUT (unchanged) my $aref_parameter_mis = $_[14]; # Replacement code of missing gene sequences -> IN (defined) / OUT (unchanged) my $href_outfile_name = $_[15]; # Outfilename of output option -> IN (defined) / OUT (unchanged) ############################## ## Print Menu Header and start info &menu ; print "\n\n\t#### FASconCAT-G: START ! ####" ; print "\n\t------------------------------------------------------------\n\n" ; ############################## ############################## ## Check if any outputformat has been chosen if ( ( $aref_parameter_fas->[0] eq 'NO' ) && ( $aref_parameter_phy->[0] eq 'NO' ) && ( $aref_parameter_nex->[0] eq 'NO' ) ){ die "\n\t!COMMAND-ERROR!: No output format selected!\n" } ############################## ############################## ## Definement of global variabels used in these subroutine and further sub-subroutines my ( %hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences (e.g. infile_1 = taxon1, sequence_of_taxon1, taxon2, sequence_of_taxon2, taxon3....) %taxa_all_files, # key: taxon name; value : number of occurence in infiles %hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value @input_files, # list of input files found in fas, FASTA, phy, or aln format $structure_seq # defined if structure sequence present in infiles ) ; ############################## ############################## ## READ IN of possible infile names (CLUSTAL, FASTA, PHYLIP formatted files) ## Store file names in @input_files for my $format ( qw/aln phy FASTA fas fasta/ ){ for my $file_input ( <*.$format> ){ push @input_files, $file_input } } ############################## checked ! ############################## ## If only single, user specified infiles should be concatenated ## open file request via FASconCAT menu and store only user defined infiles in @input_files if ( $aref_parameter_all->[0] eq 'NO' ){ &single_define ( \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (unchanged) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (unchanged) \@$aref_parameter_phy, # List of supermatrix parameter options of PHYLIP print OUT -> IN (defined) / OUT (unchanged) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (unchanged) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (unchanged) \@$aref_parameter_fil, # List of of file handling -> IN (defined) / OUT (unchanged) \@$aref_parameter_fas, # List of supermatrix parameter options of FASTA print OUT -> IN (defined) / OUT (unchanged) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (unchanged) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (unchanged) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (unchanged) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (unchanged) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (unchanged) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (unchanged) \@$aref_parameter_pro, # Start prottest analyses for aa data -> IN (defined) / OUT (unchanged) \@$aref_parameter_mis, # Replacement code of missing gene sequences -> IN (defined) / OUT (unchanged) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) ***@***.***_files # list of input files found in fas, FASTA, phy, or aln format -> IN (defined) / OUT (unchanged) ); } ############################## ############################################################ START FILE READ IN & FILE CHECK ## READ IN file content and check for correct format of infiles -> &input_check &input_check ( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (undefined) / OUT (defined) \%taxa_all_files, # key: taxon name; value : number of occurence in infiles -> IN (undefined) / OUT (defined) ***@***.***_files, # list of input files found in fas, FASTA, phy, or aln format -> IN (defined) / OUT (unchanged) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (undefined) / OUT (defined) \$structure_seq # defined if structure sequence present in infiles -> IN (undefined) / OUT (defined) ) ; ############################################################ END FILE READ IN & FILE CHECK ############################################################ START SEQ RENAMING unless ( $aref_parameter_ren->[0] eq 'NO' ){ &seq_renaming( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (changed) \%taxa_all_files, # key: taxon name; value : number of occurence in infiles -> IN (defined) / OUT (changed) \$structure_seq # defined if structure sequence present in infiles -> IN (defined) / OUT (changed) ); } ############################################################ END SEQ RENAMING ############################################################ START SEQ TRANSLATION unless ( $aref_parameter_tra->[0] eq 'NO' ){ &seq_translation( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (changed) \$aref_parameter_tra->[0] # defined ry coding parameter option -> IN (defined) / OUT (unchanged) ); } ############################################################ END SEQ TRANSLATION ############################################################ START CONSENSUS PROCESS OF SEQUENCE BLOCKS IF DEFINED ## If consensus setup is set to yes ('Freq', 'Maj', or 'Strict') built consensus sequence of defined sequence blocks (sequences with identic taxon names before the first underscore) ## regarded to chosen consensus option and store consensus sequence of defined sequence blocks in... ## ...%consensus_seq_of_taxon -> key consensus taxon name (original taxon prefix before first underscore with additional '_consensus' suffix); value: consensus sequence ## ----------------- ## e.g.: ## tax1_allel_0 -> ACGTTTTCGTTT... ## tax1_allel_1 -> ACGTTTTAATTT... ## tax1_allel_2 -> ACGTTTTGCTTT... ## tax1 -> ACGTTTTTTTTT... ## $consensus_seq_of_taxon{tax1_consensus} = ACGTTTTNNTTT... ## ----------------- ## Consensus sequence built in subroutine -> &make_consensus unless ( $aref_parameter_con->[0] eq 'NO' ){ ############################## ## Create consensus sequences of defined sequence blocks in given infile &make_consensus ( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \$aref_parameter_con->[0], # defined consensus parameter (Freq, Maj, or Strict) -> IN (defined) / OUT (unchanged) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (unchanged) \%taxa_all_files, # key: taxon name; value : number of occurence in infiles -> IN (defined) / OUT (changed) ) ############################## } ############################################################ END CONSENSUS PROCESS OF SEQUENCE BLOCKS IF DEFINED ############################################################ START RY CODING ## If defined, RY coding of either complete nucleotide sequences or 3rd positions of nuc sequences unless ( $aref_parameter_ryc->[0] eq 'NO' ){ &ry_coding( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (unchanged) \$aref_parameter_ryc->[0] # defined ry coding parameter option -> IN (defined) / OUT (unchanged) ) ; } ############################################################ END RY CODING ############################################################ START REMOVING 3RD SEQUENCE POSITION ## If defined, remove third sequence position (only in nucleotide data) unless ( $aref_parameter_3rd->[0] eq 'Remain' ){ &reject_third_nuc_position( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (changed) ) ; } ############################################################ START REMOVING 3RD SEQUENCE POSITION ########################################################### START SEQUENCE CONCATENATION ## Sequence concatenation and extraction of basal sequence information ## unless file handling parameter is set to 'Convert' -> Convert single files to other output format without adding missing sequences unless ( $aref_parameter_fil->[0] eq 'Convert' ){ &concatenate ( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (undefined) / OUT (defined) \%taxa_all_files, # key: taxon name; value : number of occurence in infiles -> IN (defined) / OUT (unchanged) \$structure_seq, # defined if structure sequence present in infiles -> IN (defined) / OUT (unchanged) \$aref_parameter_mis->[0], # defined replacement parameter (MISSING or INDEL) -> IN (defined) / OUT (unchanged) ) } ########################################################### END SEQUENCE CONCATENATION ############################################################ START PROTTEST ## If defined, RY coding of either complete nucleotide sequences or 3rd positions of nuc sequences unless ( $aref_parameter_pro->[0] eq 'NO' ){ unless ( ( $aref_parameter_fas->[0] eq 'NO' ) && ( $aref_parameter_phy->[0] eq 'NO' ) ){ &start_prottest( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (changed) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (unchanged) \$aref_parameter_fil->[0], # List of of file handling -> IN (defined) / OUT (unchanged) \$aref_parameter_prt->[0], # Print partition files for concatenated data -> IN (defined) / OUT (unchanged) \$href_outfile_name->{prottest}, # PROTTEST SCRIPT NAME -> IN (defined) / OUT (unchanged) ) ; } else{ print "\n\n\t!COMMAND-ERROR!: ProtTest not started!\n\tFasta or phylip outfile format must be defined for ProtTest analyses!\n" } } ############################################################ END PROTTEST ############################## ## If defined nexus output set additional info option to 'all info' -> 'YES' if ( $aref_parameter_nex->[0] =~ /BLOCK|MrBAYES/ ){ $aref_parameter_inf->[0] = 'YES' } ############################## ############################################################ START STRUCTURE SEQUENCE ANALYSIS ## If additional parameter info option set to yes and defined structure sequence found in infiles ## extract structure sequence info like loop and stem positions; N of states... if ( ( $aref_parameter_inf->[0] eq 'YES' ) && ( $structure_seq ) ){ &structure_handling ( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (unchanged) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (changed) ) ; } ############################################################ END STRUCTURE SEQUENCE ANALYSIS ############################################################ START EXTRACTION OF ADDITIONAL SEQUENCE STATE INFO ## Count additional info about number of character states for each file sorted by missing data, ambiguity, indel event, and informative state ## if additional info options is set to 'YES' if ( $aref_parameter_inf->[0] eq "YES" ){ &get_info ( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (unchanged) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (changed) ) ; } ############################################################ END EXTRACTION OF ADDITIONAL SEQUENCE STATE INFO ############################################################ START PRINT OUT OF SUPERMATRIX & EXTRACTED INFO ## Print OUT outfiles &print_out ( \%hol_seq_of_tax_of_infile, # key: input file name; value ; list of taxa and corresponding sequences -> IN (defined) / OUT (unchanged) \%hoh_info_of_infile_of_type, # key1: infilename, key2: type of info (e.g. 'seqlength'); info type associated value -> IN (defined) / OUT (unchanged) \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged) \@$aref_parameter_all, # List of parameter options of data concatenation -> IN (defined) / OUT (unchanged) \@$aref_parameter_inf, # List of parameter options of info print out -> IN (defined) / OUT (unchanged) \@$aref_parameter_phy, # List of parameter options of PHYLIP print OUT -> IN (defined) / OUT (unchanged) \@$aref_parameter_nex, # List of supermatrix parameter options of NEXUS print OUT -> IN (defined) / OUT (unchanged) \@$aref_parameter_con, # List of consensus options -> IN (defined) / OUT (unchanged) \@$aref_parameter_fil, # List of filehandling options -> IN (defined) / OUT (unchanged) \@$aref_parameter_fas, # List of parameter options of FASTA print OUT -> IN (defined) / OUT (unchanged) \@$aref_parameter_3rd, # List of third position handling -> IN (defined) / OUT (unchanged) \@$aref_parameter_ryc, # List of RY coding -> IN (defined) / OUT (unchanged) \@$aref_parameter_tra, # List of sequence translation options -> IN (defined) / OUT (unchanged) \@$aref_parameter_par, # Print parsimonious sites as extra msa file -> IN (defined) / OUT (unchanged) \@$aref_parameter_ren, # Rename taxon names of given ifiles -> IN (defined) / OUT (unchanged) \@$aref_parameter_prt, # Print partition files for concatenated data -> IN (defined) / OUT (unchanged) \@$aref_parameter_pro, # Start prottest analyses for aa data -> IN (defined) / OUT (unchanged) \@$aref_parameter_mis, # Replacement code of missing gene sequences -> IN (defined) / OUT (unchanged) \$structure_seq # defined if structure sequence present in infiles -> IN (defined) / OUT (unchanged) ) ; ############################################################ END PRINT OUT OF SUPERMATRIX & EXTRACTED INFO ############################################################ START PRINT OUT OF SUPERMATRIX & EXTRACTED INFO ## Print END section on terminal &end ( \%$href_outfile_name, # Outfilename of output option -> IN (defined) / OUT (unchanged)

[Anna-pro]

Thank you! I tried to re-run my analysis with the updated FASconCAT-G_v1.04.pl from above, but it aborted with some errors:

Operator or semicolon missing before *_mis at FASconCAT-G_v1.04.pl line 82.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 82.
Operator or semicolon missing before *_all at FASconCAT-G_v1.04.pl line 99.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 99.
Operator or semicolon missing before *_info at FASconCAT-G_v1.04.pl line 100.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 100.
Operator or semicolon missing before *_phy at FASconCAT-G_v1.04.pl line 101.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 101.
Operator or semicolon missing before *_nex at FASconCAT-G_v1.04.pl line 102.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 102.
Operator or semicolon missing before *_con at FASconCAT-G_v1.04.pl line 103.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 103.
Operator or semicolon missing before *_file at FASconCAT-G_v1.04.pl line 104.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 104.
Operator or semicolon missing before *_fas at FASconCAT-G_v1.04.pl line 105.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 105.
Operator or semicolon missing before *_3rd at FASconCAT-G_v1.04.pl line 106.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 106.
Operator or semicolon missing before *_ryc at FASconCAT-G_v1.04.pl line 107.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 107.
Operator or semicolon missing before *_tra at FASconCAT-G_v1.04.pl line 108.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 108.
Operator or semicolon missing before *_par at FASconCAT-G_v1.04.pl line 109.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 109.
Operator or semicolon missing before *_ren at FASconCAT-G_v1.04.pl line 110.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 110.
Operator or semicolon missing before *_prt at FASconCAT-G_v1.04.pl line 111.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 111.
Operator or semicolon missing before *_pro at FASconCAT-G_v1.04.pl line 112.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 112.
Operator or semicolon missing before *_mis at FASconCAT-G_v1.04.pl line 113.
Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 113.
syntax error at FASconCAT-G_v1.04.pl line 68, near "**."
syntax error at FASconCAT-G_v1.04.pl line 99, near "**."
Global symbol "@argv" requires explicit package name (did you forget to declare "my @argv"?) at FASconCAT-G_v1.04.pl line 147.
BEGIN not safe after errors--compilation aborted at FASconCAT-G_v1.04.pl line 870.

[PatrickKueck]

That's strange. I crosschecked the version I send you in the last email and the script works fine on my system. However, what I can see from your error-message is that you have apparently used the old version 1.04. Although your error prompts do not make much sense in 1.04 too. Please, can you verify that you have used the actual 1.05 version and restart the analysis. Please, also delete in advance all former fasconcat output files that you got from your previous start attempts.   If FASconCAT is still not running, please send me the commandline that you have used. Furthermore, it would be great if you could tell me which operating system and perl interpreter you use.   Best   Patrick         Gesendet: Dienstag, 19. April 2022 um 17:10 Uhr Von: "Anna-pro" ***@***.***> An: "PatrickKueck/FASconCAT-G" ***@***.***> Cc: "Patrick Kueck" ***@***.***>, "Comment" ***@***.***> Betreff: Re: [PatrickKueck/FASconCAT-G] Output with [X] symbol, wrong identification of data type (Issue #11)   Thank you! I tried to re-run my analysis with the updated FASconCAT-G_v1.04.pl from above, but it aborted with some errors: Operator or semicolon missing before *_mis at FASconCAT-G_v1.04.pl line 82. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 82. Operator or semicolon missing before *_all at FASconCAT-G_v1.04.pl line 99. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 99. Operator or semicolon missing before *_info at FASconCAT-G_v1.04.pl line 100. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 100. Operator or semicolon missing before *_phy at FASconCAT-G_v1.04.pl line 101. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 101. Operator or semicolon missing before *_nex at FASconCAT-G_v1.04.pl line 102. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 102. Operator or semicolon missing before *_con at FASconCAT-G_v1.04.pl line 103. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 103. Operator or semicolon missing before *_file at FASconCAT-G_v1.04.pl line 104. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 104. Operator or semicolon missing before *_fas at FASconCAT-G_v1.04.pl line 105. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 105. Operator or semicolon missing before *_3rd at FASconCAT-G_v1.04.pl line 106. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 106. Operator or semicolon missing before *_ryc at FASconCAT-G_v1.04.pl line 107. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 107. Operator or semicolon missing before *_tra at FASconCAT-G_v1.04.pl line 108. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 108. Operator or semicolon missing before *_par at FASconCAT-G_v1.04.pl line 109. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 109. Operator or semicolon missing before *_ren at FASconCAT-G_v1.04.pl line 110. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 110. Operator or semicolon missing before *_prt at FASconCAT-G_v1.04.pl line 111. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 111. Operator or semicolon missing before *_pro at FASconCAT-G_v1.04.pl line 112. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 112. Operator or semicolon missing before *_mis at FASconCAT-G_v1.04.pl line 113. Ambiguous use of * resolved as operator * at FASconCAT-G_v1.04.pl line 113. syntax error at FASconCAT-G_v1.04.pl line 68, near "**." syntax error at FASconCAT-G_v1.04.pl line 99, near "**." Global symbol ***@***.***" requires explicit package name (did you forget to declare "my @argv"?) at FASconCAT-G_v1.04.pl line 147. BEGIN not safe after errors--compilation aborted at FASconCAT-G_v1.04.pl line 870. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>