Tools that could be updated

## Tools that could be updated

| Tool | Current Version | Latest Upstream | Source |
|------|----------------|-----------------|--------|
| [adapterremoval](https://github.com/evolbioinfo/dockerfiles/tree/main/adapterremoval) | `v2.3.4` | `v3.0.0` | [MikkelSchubert/adapterremoval](https://github.com/MikkelSchubert/adapterremoval) (GitHub) |
| [bbmap](https://github.com/evolbioinfo/dockerfiles/tree/main/bbmap) | `v39.81` | `39.85` | [bbmap](https://sourceforge.net/projects/bbmap/) (SourceForge) |
| [bwa-mem](https://github.com/evolbioinfo/dockerfiles/tree/main/bwa-mem) | `v2.2.1` | `v2.3` | [bwa-mem2/bwa-mem2](https://github.com/bwa-mem2/bwa-mem2) (GitHub) |
| [civet](https://github.com/evolbioinfo/dockerfiles/tree/main/civet) | `v2.1.2` | `v3.0` | [artic-network/civet](https://github.com/artic-network/civet) (GitHub) |
| [hyphy](https://github.com/evolbioinfo/dockerfiles/tree/main/hyphy) | `v2.5.97` | `2.5.98` | [veg/hyphy](https://github.com/veg/hyphy) (GitHub) |
| [iqtree](https://github.com/evolbioinfo/dockerfiles/tree/main/iqtree) | `v3.1.1` | `v3.1.2` | [iqtree/iqtree3](https://github.com/iqtree/iqtree3) (GitHub) |
| [irma](https://github.com/evolbioinfo/dockerfiles/tree/main/irma) | `v1.3.1` | `v1.3.3` | [CDCgov/irma](https://github.com/CDCgov/irma) (GitHub) |
| [jq](https://github.com/evolbioinfo/dockerfiles/tree/main/jq) | `v1.8.1` | `jq-1.8.1` | [stedolan/jq](https://github.com/stedolan/jq) (GitHub) |
| [lsd2](https://github.com/evolbioinfo/dockerfiles/tree/main/lsd2) | `v2.4.1` | `v.2.4.1` | [tothuhien/lsd2](https://github.com/tothuhien/lsd2) (GitHub) |
| [maple](https://github.com/evolbioinfo/dockerfiles/tree/main/maple) | `v0.7.5` | `MAPLEv0.7.5` | [NicolaDM/MAPLE](https://github.com/NicolaDM/MAPLE) (GitHub) |
| [pangolin](https://github.com/evolbioinfo/dockerfiles/tree/main/pangolin) | `v3.1.16` | `v4.4` | [cov-lineages/pangolin](https://github.com/cov-lineages/pangolin) (GitHub) |
| [rappas](https://github.com/evolbioinfo/dockerfiles/tree/main/rappas) | `v1.21` | `v1.22` | [phylo42/RAPPAS](https://github.com/phylo42/RAPPAS) (GitHub) |
| [raxml-ng](https://github.com/evolbioinfo/dockerfiles/tree/main/raxml-ng) | `v2.0.0` | `2.0.1` | [amkozlov/raxml-ng](https://github.com/amkozlov/raxml-ng) (GitHub) |
| [schmutzi](https://github.com/evolbioinfo/dockerfiles/tree/main/schmutzi) | `v1.5.6` | `v1.5.7` | [grenaud/schmutzi](https://github.com/grenaud/schmutzi) (GitHub) |
| [snakemake](https://github.com/evolbioinfo/dockerfiles/tree/main/snakemake) | `v9.17.2` | `9.21.0` | [snakemake](https://pypi.org/project/snakemake/) (PyPI) |
| [sra-tools](https://github.com/evolbioinfo/dockerfiles/tree/main/sra-tools) | `v3.0.1` | `VDB-4760-2.9.7` | [ncbi/sra-tools](https://github.com/ncbi/sra-tools) (GitHub) |
| [tcoffee](https://github.com/evolbioinfo/dockerfiles/tree/main/tcoffee) | `Version_13.46.2.7c9e712d` | `v12.00` | [cbcrg/tcoffee](https://github.com/cbcrg/tcoffee) (GitHub) |
| [treetime](https://github.com/evolbioinfo/dockerfiles/tree/main/treetime) | `v0.11.4` | `v0.12.1` | [neherlab/treetime](https://github.com/neherlab/treetime) (GitHub) |
| [trimgalore](https://github.com/evolbioinfo/dockerfiles/tree/main/trimgalore) | `v0.6.11` | `v2.2.0` | [FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore) (GitHub) |

## Tools where the version could not be determined

| Tool | Current Version | Reason |
|------|----------------|--------|
| [admixture](https://github.com/evolbioinfo/dockerfiles/tree/main/admixture) | `v1.3.1` | No upstream source found in Dockerfile |
| [bayestraits](https://github.com/evolbioinfo/dockerfiles/tree/main/bayestraits) | `v5.0.3` | Could not fetch upstream version from GitHub |
| [clustal_omega](https://github.com/evolbioinfo/dockerfiles/tree/main/clustal_omega) | `v1.2.4` | No upstream source found in Dockerfile |
| [deseq](https://github.com/evolbioinfo/dockerfiles/tree/main/deseq) | `v1.39.0` | No upstream source found in Dockerfile |
| [fastcodeml](https://github.com/evolbioinfo/dockerfiles/tree/main/fastcodeml) | `v1.1.0` | Could not fetch upstream version from GitLab |
| [finestructure](https://github.com/evolbioinfo/dockerfiles/tree/main/finestructure) | `v4.1.1` | No upstream source found in Dockerfile |
| [gblocks](https://github.com/evolbioinfo/dockerfiles/tree/main/gblocks) | `v1.0` | No upstream source found in Dockerfile |
| [guppy](https://github.com/evolbioinfo/dockerfiles/tree/main/guppy) | `v3.1.5` | No upstream source found in Dockerfile |
| [hmmer](https://github.com/evolbioinfo/dockerfiles/tree/main/hmmer) | `v3.4` | No upstream source found in Dockerfile |
| [igv](https://github.com/evolbioinfo/dockerfiles/tree/main/igv) | `v2.9.0` | No upstream source found in Dockerfile |
| [jphmm](https://github.com/evolbioinfo/dockerfiles/tree/main/jphmm) | `v03.2015` | No upstream source found in Dockerfile |
| [label](https://github.com/evolbioinfo/dockerfiles/tree/main/label) | `v0.6.4` | No upstream source found in Dockerfile |
| [lastal](https://github.com/evolbioinfo/dockerfiles/tree/main/lastal) | `v980` | No upstream source found in Dockerfile |
| [multiqc](https://github.com/evolbioinfo/dockerfiles/tree/main/multiqc) | `v1.10` | No upstream source found in Dockerfile |
| [newick_utilities](https://github.com/evolbioinfo/dockerfiles/tree/main/newick_utilities) | `v1.6` | Could not fetch upstream version from GitHub |
| [nextstrain-base](https://github.com/evolbioinfo/dockerfiles/tree/main/nextstrain-base) | `build-20251119T000157Z` | No upstream source found in Dockerfile |
| [noisy](https://github.com/evolbioinfo/dockerfiles/tree/main/noisy) | `v1.5.12` | No upstream source found in Dockerfile |
| [paml](https://github.com/evolbioinfo/dockerfiles/tree/main/paml) | `v4.8a` | No upstream source found in Dockerfile |
| [papara](https://github.com/evolbioinfo/dockerfiles/tree/main/papara) | `v2.5` | Could not fetch upstream version from GitHub |
| [phyml-sms](https://github.com/evolbioinfo/dockerfiles/tree/main/phyml-sms) | `v1.8.1.1` | No upstream source found in Dockerfile |
| [predicthaplo](https://github.com/evolbioinfo/dockerfiles/tree/main/predicthaplo) | `v1.0` | No upstream source found in Dockerfile |
| [ptp](https://github.com/evolbioinfo/dockerfiles/tree/main/ptp) | `v4bb2daf` | Could not fetch upstream version from GitHub |
| [sphinx](https://github.com/evolbioinfo/dockerfiles/tree/main/sphinx) | `v1.8.5` | No upstream source found in Dockerfile |
| [sratoolkit](https://github.com/evolbioinfo/dockerfiles/tree/main/sratoolkit) | `v3.0.1` | No upstream source found in Dockerfile |
| [stringtie](https://github.com/evolbioinfo/dockerfiles/tree/main/stringtie) | `v2.2.1` | No upstream source found in Dockerfile |
| [tqdist](https://github.com/evolbioinfo/dockerfiles/tree/main/tqdist) | `v1.0.2` | No upstream source found in Dockerfile |
| [velvet](https://github.com/evolbioinfo/dockerfiles/tree/main/velvet) | `v1.2.10` | No upstream source found in Dockerfile |
| [vivan](https://github.com/evolbioinfo/dockerfiles/tree/main/vivan) | `v0.43` | No upstream source found in Dockerfile |
| [wget](https://github.com/evolbioinfo/dockerfiles/tree/main/wget) | `v1.17.1` | No upstream source found in Dockerfile |

---
*Last checked: 2026-05-18 11:50 UTC*

Tool	Current Version	Latest Upstream	Source
adapterremoval	`v2.3.4`	`v3.0.0`	MikkelSchubert/adapterremoval (GitHub)
bbmap	`v39.81`	`39.85`	bbmap (SourceForge)
bwa-mem	`v2.2.1`	`v2.3`	bwa-mem2/bwa-mem2 (GitHub)
civet	`v2.1.2`	`v3.0`	artic-network/civet (GitHub)
hyphy	`v2.5.97`	`2.5.98`	veg/hyphy (GitHub)
iqtree	`v3.1.1`	`v3.1.2`	iqtree/iqtree3 (GitHub)
irma	`v1.3.1`	`v1.3.3`	CDCgov/irma (GitHub)
jq	`v1.8.1`	`jq-1.8.1`	stedolan/jq (GitHub)
lsd2	`v2.4.1`	`v.2.4.1`	tothuhien/lsd2 (GitHub)
maple	`v0.7.5`	`MAPLEv0.7.5`	NicolaDM/MAPLE (GitHub)
pangolin	`v3.1.16`	`v4.4`	cov-lineages/pangolin (GitHub)
rappas	`v1.21`	`v1.22`	phylo42/RAPPAS (GitHub)
raxml-ng	`v2.0.0`	`2.0.1`	amkozlov/raxml-ng (GitHub)
schmutzi	`v1.5.6`	`v1.5.7`	grenaud/schmutzi (GitHub)
snakemake	`v9.17.2`	`9.21.0`	snakemake (PyPI)
sra-tools	`v3.0.1`	`VDB-4760-2.9.7`	ncbi/sra-tools (GitHub)
tcoffee	`Version_13.46.2.7c9e712d`	`v12.00`	cbcrg/tcoffee (GitHub)
treetime	`v0.11.4`	`v0.12.1`	neherlab/treetime (GitHub)
trimgalore	`v0.6.11`	`v2.2.0`	FelixKrueger/TrimGalore (GitHub)

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Tools that could be updated #21