Updated Docs and ReadME

README.md

@@ -32,7 +32,8 @@
 
 ## <a name="intro"></a> Introduction
 
-DIPPER (**DI**stance-based **P**hylogenetic **P**lac**ER**) is a tool for ultrafast and ultralarge phylogenetic reconstruction on GPUs, designed to maintain high accuracy with a minimal memory footprint. DIPPER introduces several innovations, including a divide-and-conquer strategy, a new placement algorithm, and an on-the-fly distance calculator that dynamically enables selective distance computation. DIPPER supports tree reconstruction with zero violations even from non-additive distance matrices and a faster heuristic mode with significantly fewer violations than baseline tools. 
+DIPPER (**DI**stance-based **P**hylogenetic **P**lac**ER**) is a tool for ultrafast and ultralarge phylogenetic reconstruction on GPUs, designed to maintain high accuracy with a minimal memory footprint. DIPPER introduces several innovations, including a divide-and-conquer strategy, a new placement algorithm, and an on-the-fly distance calculator that dynamically enables selective distance computation. In addition, DIPPER addresses the common issue of evolutionary distance underestimation observed in earlier methods—significantly reducing it in its default mode and offering a strict mode that completely eliminates the underestimation.
+
 
 ## <a name="install"></a> Installation
 NOTE: DIPPER is currently supported on systems with <b>NVIDIA GPUs only</b>. Support for additional platforms, including AMD GPUs and CPU-only options for x86-64 and ARM64 architecture, will be added soon. Stay tuned!

docs/index.md

@@ -5,16 +5,14 @@
 
 ## <b>Introduction</b> 
 ### <b>Overview</b><a name="overview"></a>
-DIPPER (**DI**stance-based **P**hylogenetic **P**lac**ER**) is an ultrafast tool designed to reconstruct ultralarge phylogenies. 
+
+DIPPER (**DI**stance-based **P**hylogenetic **P**lac**ER**) is a tool for ultrafast and ultralarge phylogenetic reconstruction on GPUs, designed to maintain high accuracy with a minimal memory footprint. DIPPER introduces several innovations, including a divide-and-conquer strategy, a new placement algorithm, and an on-the-fly distance calculator that dynamically enables selective distance computation. In addition, DIPPER addresses the common issue of evolutionary distance underestimation observed in earlier methods—significantly reducing it in its default mode and offering a strict mode that completely eliminates the underestimation. 
 
 <div align="center">
     <div><b>Figure 1: Overview of DIPPER algorithm</b></div>
     <img src="images/overview.png" width="1000"/>
 </div>
 
-### <b>Key Features</b>
-
-#### TBA
 
 <a name="install"></a>
 ## <b>Installation Methods</b>
@@ -115,7 +113,7 @@ cd bin
 | `-I`, `--input-file`     | Input file path <b>(required)</b>:<br>PHYLIP for distance matrix, FASTA for MSA or raw sequences                                   |
 | `-O`, `--output-file`    | Output file path <b>(required)</b>                                                                                                |
 | `-m`, `--algorithm`      | Algorithm selection:<br>`0` - auto <b>(default)</b><br>`1` - force placement<br>`2` - force NJ<br>`3` - divide-and-conquer     |
-| `-p`, `--placement-mode` | Placement mode:<br>`0` - exact<br>`1` - k-closest <b>(default)</b>                                                      |
+| `-K`, `--K-closest` | Placement mode:<br>`-1` - exact<br>`10` - <b>default</b>                                                      |
 | `-k`, `--kmer-size`      | K-mer size (Valid range: 2–15, <b>default: 15</b>)                                                                      |
 | `-s`, `--sketch-size`    | Sketch size (<b>default: 1000</b>)                                                                                    |
 | `-d`, `--distance-type`  | Distance type:<br>`1` - uncorrected<br>`2` - JC <b>(default)</b> <br>`3` - Tajima-Nei<br>`4` - K2P<br>`5` - Tamura<br>`6` - Jinnei |

src/tree_generation.cu

@@ -64,10 +64,10 @@ void parseArguments(int argc, char** argv)
         "  2 - force conventional NJ\n"
         "  3 - force divide-and-conquer")
 
-        ("placement-mode,p",   po::value<std::string>(),
+        ("--K-closest,K",   po::value<std::string>(),
         "Placement mode:\n"
-        "  0 - exact mode\n"
-        "  1 - k-closest mode (default)")
+        "  -1 - exact mode\n"
+        "  10 - default")
 
         ("kmer-size,k",        po::value<std::string>(),
         "K-mer size:\n"
@@ -219,8 +219,8 @@ int main(int argc, char** argv) {
     try {algo = vm["algorithm"].as<std::string>();}
     catch(std::exception &e){}
 
-    std::string placemode = "1";
-    try {placemode = vm["placement-mode"].as<std::string>();}
+    std::string placemode = "10";
+    try {placemode = vm["K-closest"].as<std::string>();}
     catch(std::exception &e){}
 
     bool add = false;
@@ -376,7 +376,7 @@ int main(int argc, char** argv) {
         MashPlacement::msaDeviceArrays.allocateDeviceArrays(fourBitCompressedSeqs, seqLengths, numSequences, params);
         if(algo=="1"||algo=="0"&&numSequences>=placement_thr&&numSequences<dc_thr){
             std::cerr<<"Using ";
-            if(placemode=="0"){
+            if(placemode=="-1"){
                 std::cerr<<" exact placement mode\n";
                 MashPlacement::placementDeviceArrays.allocateDeviceArrays(numSequences);
                 auto createArrayEnd = std::chrono::high_resolution_clock::now();
@@ -513,7 +513,7 @@ int main(int argc, char** argv) {
             auto createSketchEnd = std::chrono::high_resolution_clock::now();
             std::chrono::nanoseconds createSketchTime = createSketchEnd - createSketchStart; 
             std::cerr << "Sketch Created in: " <<  createSketchTime.count()/1000000 << " ms\n";
-            if(placemode=="0"){
+            if(placemode=="-1"){
                 std::cerr<<"Using exact placement mode\n";
                 MashPlacement::placementDeviceArrays.allocateDeviceArrays(numSequences);
                 auto createTreeStart = std::chrono::high_resolution_clock::now();
@@ -611,7 +611,7 @@ int main(int argc, char** argv) {
         fgets(temp, 20, filePtr);
         MashPlacement::matrixReader.allocateDeviceArrays(numSequences, filePtr);
         if(algo=="1"||algo=="0"&&numSequences>=placement_thr&&numSequences<dc_thr){
-            if(placemode=="0"){
+            if(placemode=="-1"){
                 std::cerr<<"Using exact placement mode\n";
                 MashPlacement::placementDeviceArrays.allocateDeviceArrays(numSequences);
                 MashPlacement::placementDeviceArrays.findPlacementTree(params, MashPlacement::mashDeviceArrays, MashPlacement::matrixReader, MashPlacement::msaDeviceArrays);