{"id":17844838,"url":"https://github.com/dombennett/project-dormouse","last_synced_at":"2025-10-17T03:34:30.145Z","repository":{"id":30180126,"uuid":"33730684","full_name":"DomBennett/Project-dormouse","owner":"DomBennett","description":":mouse: Mini phylogenetic analysis of dormouse tapeworm samples","archived":false,"fork":false,"pushed_at":"2016-01-06T14:21:12.000Z","size":25,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-02-08T06:13:03.966Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/DomBennett.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-04-10T13:46:00.000Z","updated_at":"2015-07-08T14:38:42.000Z","dependencies_parsed_at":"2022-08-28T18:34:26.548Z","dependency_job_id":null,"html_url":"https://github.com/DomBennett/Project-dormouse","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-dormouse","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-dormouse/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-dormouse/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/DomBennett%2FProject-dormouse/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/DomBennett","download_url":"https://codeload.github.com/DomBennett/Project-dormouse/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246837685,"owners_count":20841903,"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":[],"created_at":"2024-10-27T21:33:12.285Z","updated_at":"2025-10-17T03:34:25.098Z","avatar_url":"https://github.com/DomBennett.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Phylogenetic analysis of dormouse tapeworm samples\n\nPipeline for determining species of tapeworm discovered in Hazel dormouse (*Muscardinus avellanarius*) using 18S and 28S PCR amplified sequences.\n\n### Stages\n\n1. NCBI BLAST amplified sequences against Cyclophellyidea species (txid6201) [MANUALLY]\n2. NCBI BLAST amplified sequences against Caryophyllidea species (txid108240) [MANUALLY]\n3. Align with MAFFT-QINISI each amplified sequence against BLAST results\n4. Combine into single supermatrix\n5. Use RAxML to create tree with Caryophyllidea outgroup and partition by gene\n\nThe scripts provided here perform stages 3-4. Original data not provided.\n\n### Requirements\n\n* Python\n* Biopython\n* MAFFT\n* RAxML\n* UNIX\n\n### Running\n\n```{bash}\nrun.sh \u003e\u0026 log.txt\n```\n\n### Dir structure\n```\n-- run.sh\n-- 1_sequences/\n-- 2_alignments/\n-- 3_trees/\n-- python_scripts/\n  -- sort_names.py\n    -- [converts the names of each in the blast results to species names for tree]\n  -- combine.py\n    -- [combines the results of each alignment BLAST results intoa single supermatrix]\n-- data/\n  -- samples/\n    -- [PCR amplified sequences from dormouse sample]\n  -- BLAST_results/\n    -- [Top 100 BLAST results for each amplified sequence constrained to the Cyclophyllidea, and then Caryophyllidea (outgroup). We used megablast with default parameters.]\n-- misc/\n    -- all_cyclophyllidea_18s_sequences.fasta\n      -- [Downloaded all 18S sequences for Cyclophyllidea (tapeworms) NCBI nucleotide search term: \"txid6201[Organism:exp] AND 18S NOT predicted[TI] NOT shotgun[TI] NOT scaffold[TI] NOT assembly[TI] NOT unverified[TI]\"]\n    -- primer_pairs.fasta\n      -- [the primer pairs for 18S that Gaby sequenced from the Dormouse sample]\n\n```\n\n### Run history\nBLAST results were downloaded from NCBI manually from 04-05/2015\n\nrun.sh was run on Imperial College London's bioinformatics server: codon.bioinformatics.ic.ac.uk (05/2015)\n\n### Author\nDom Bennett\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-dormouse","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdombennett%2Fproject-dormouse","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdombennett%2Fproject-dormouse/lists"}