Tools that could be updated

## Tools that could be updated

| Tool | Current Version | Latest Upstream | Source |
|------|----------------|-----------------|--------|
| [bbmap](https://github.com/evolbioinfo/dockerfiles/tree/main/bbmap) | `v39.80` | `39.81` | [bbmap](https://sourceforge.net/projects/bbmap/) (SourceForge) |
| [civet](https://github.com/evolbioinfo/dockerfiles/tree/main/civet) | `v2.1.2` | `v3.0` | [artic-network/civet](https://github.com/artic-network/civet) (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) |
| [schmutzi](https://github.com/evolbioinfo/dockerfiles/tree/main/schmutzi) | `v1.5.6` | `v1.5.7` | [grenaud/schmutzi](https://github.com/grenaud/schmutzi) (GitHub) |
| [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) |

## 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 |
| [phylodeep](https://github.com/evolbioinfo/dockerfiles/tree/main/phylodeep) | `v0.9` | No upstream source found in Dockerfile |
| [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 |
| [snakemake](https://github.com/evolbioinfo/dockerfiles/tree/main/snakemake) | `v9.17.2` | No upstream source found in Dockerfile |
| [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 |
| [treesimulator](https://github.com/evolbioinfo/dockerfiles/tree/main/treesimulator) | `v0.2.27` | 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: 2026-03-30 09:22 UTC*

Tool	Current Version	Latest Upstream	Source
bbmap	`v39.80`	`39.81`	bbmap (SourceForge)
civet	`v2.1.2`	`v3.0`	artic-network/civet (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)
schmutzi	`v1.5.6`	`v1.5.7`	grenaud/schmutzi (GitHub)
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)

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Tools that could be updated #18