{"id":20074777,"url":"https://github.com/greenelab/continuous_analysis_phylo","last_synced_at":"2025-06-12T05:07:55.376Z","repository":{"id":79359284,"uuid":"64413174","full_name":"greenelab/continuous_analysis_phylo","owner":"greenelab","description":"A simple phylogenetic tree building example of Continuous Analysis","archived":false,"fork":false,"pushed_at":"2016-08-19T14:40:12.000Z","size":854,"stargazers_count":4,"open_issues_count":0,"forks_count":2,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-05-23T00:26:39.072Z","etag":null,"topics":["analysis","continuous-integration","example","methodology","workflow"],"latest_commit_sha":null,"homepage":"http://dx.doi.org/10.1101/056473","language":"Shell","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/greenelab.png","metadata":{"files":{"readme":"readme.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-07-28T16:58:26.000Z","updated_at":"2021-10-13T19:50:47.000Z","dependencies_parsed_at":"2023-03-11T04:01:02.501Z","dependency_job_id":null,"html_url":"https://github.com/greenelab/continuous_analysis_phylo","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/greenelab/continuous_analysis_phylo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcontinuous_analysis_phylo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcontinuous_analysis_phylo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcontinuous_analysis_phylo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcontinuous_analysis_phylo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/greenelab","download_url":"https://codeload.github.com/greenelab/continuous_analysis_phylo/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/greenelab%2Fcontinuous_analysis_phylo/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259402144,"owners_count":22851877,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["analysis","continuous-integration","example","methodology","workflow"],"created_at":"2024-11-13T14:54:19.084Z","updated_at":"2025-06-12T05:07:55.364Z","avatar_url":"https://github.com/greenelab.png","language":"Shell","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Continuous Analysis Phylogentics Example\n\nThis is a sample repository showing the [Continuous Analysis Workflow](https://github.com/greenelab/continuous_analysis). This process is described in detail and available as a [pre-print](http://biorxiv.org/content/early/2016/06/01/056473).\n\nIn this example we use several tools to build phylogenies from alignments:\n\n* [MAFFT](http://www.ebi.ac.uk/Tools/msa/mafft/)\n* [EMBOSS Seqret](http://www.ebi.ac.uk/Tools/sfc/emboss_seqret/)\n* [PHYLIP](http://evolution.genetics.washington.edu/phylip/)\n\t* [DNAPARS](http://evolution.genetics.washington.edu/phylip/doc/dnapars.html)\n\t* [Drawtree](http://evolution.genetics.washington.edu/phylip/doc/draw.html)\n\t* [Seqboot](http://evolution.genetics.washington.edu/phylip/doc/seqboot.html)\n\t* [Consense](http://evolution.genetics.washington.edu/phylip/doc/consense.html) \n* [ImageMagick](http://www.imagemagick.org/script/index.php)\n\n## Sample Results\n\nThe full analysis is described below, here we show two of the useful artifacts generated through Continuous Analysis:\n\n1. Change logs/synchronization between code and figures:\n[Live Version](https://github.com/greenelab/continuous_analysis_phylo/commit/518fc9c446e7e1feb0f08e753a945e0b10adcdec#diff-81f3f2f12d4403ba083a558b76a9d056)\n\n![](https://raw.githubusercontent.com/greenelab/continuous_analysis_phylo/master/references/compare.png)\n\n\n2. Complete \"audit\" logs of the code run:\n[Logs](https://raw.githubusercontent.com/greenelab/continuous_analysis_phylo/master/references/full_logs.txt)\n\n![](https://raw.githubusercontent.com/greenelab/continuous_analysis_phylo/master/references/logs.png)\n\n## Description of analysis\nIn this analysis we align 5 mRNA sequences and use these alignments to build phylogenies. Analysis code is available [here](https://github.com/greenelab/continuous_analysis_phylo/blob/master/run_phylo.sh)\n\n1. We look at 5 mRNA sequences (findable at: http://www.ncbi.nlm.nih.gov/nuccore)\n\t* \tTwist - Fly (NM_079092, splice form A)\n\t* \tTwist1 - Human (NM_000474)\n\t* \tTwist1 - Mouse (NM_011658)\n\t* \tTwist2 - Human (NM_057179) - Added in second commit to see differences\n\t* \tTwist2 - Mouse (NM_007855) \n\nAnd load the sequences into twist.fasta\n\n2. Align the sequences using MAFFT.\n3. Convert to PHYLIP interleaved format using EMBOSS Seqret.\n4. Calculate the maximum parsimony tree for the sequences using DNAPARS.\n5. Draw a representation fo this tree using drawtree.\n6. Use Seqboot to assess the robustness of the generated tree.\n7. Determine the consensus tree from the bootstrapped trees.\n\nWe performed this process twice, once [without HumanTwist2 and once with HumanTwist2](https://github.com/greenelab/continuous_analysis_phylo/commit/9c9d07f2e9bbbedd5d3fe81c0f6c92acf48924d3). The difference is viewable at: [results](https://github.com/greenelab/continuous_analysis_phylo/commit/518fc9c446e7e1feb0f08e753a945e0b10adcdec).\n\n\n## Feedback\n\nPlease feel free to email me - (brettbe) at med.upenn.edu with any feedback or raise a github issue with any comments or questions.\n\n## Acknowledgements\n\nWe would like to thank Katie Siewert for providing the analysis design.\n\nThis work is supported by the Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative through Grant GBMF4552 to C.S.G. as well as the Commonwealth Universal Research Enhancement (CURE) Program grant from the Pennsylvania Department of Health.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fcontinuous_analysis_phylo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgreenelab%2Fcontinuous_analysis_phylo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgreenelab%2Fcontinuous_analysis_phylo/lists"}