{"id":20844833,"url":"https://github.com/lkremer/showtree","last_synced_at":"2025-05-09T02:21:25.195Z","repository":{"id":50627676,"uuid":"93156150","full_name":"LKremer/showTree","owner":"LKremer","description":"showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.","archived":false,"fork":false,"pushed_at":"2019-03-28T08:16:53.000Z","size":67,"stargazers_count":30,"open_issues_count":0,"forks_count":8,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-31T21:27:50.309Z","etag":null,"topics":["ete3","gene-families","phylogenetic-trees","phylogenetics","protein-domains","protein-families","python","treeview","visualization"],"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/LKremer.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":"2017-06-02T10:43:30.000Z","updated_at":"2024-06-15T17:54:54.000Z","dependencies_parsed_at":"2022-09-18T06:55:22.072Z","dependency_job_id":null,"html_url":"https://github.com/LKremer/showTree","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/LKremer%2FshowTree","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FshowTree/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FshowTree/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/LKremer%2FshowTree/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/LKremer","download_url":"https://codeload.github.com/LKremer/showTree/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253176669,"owners_count":21866185,"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":["ete3","gene-families","phylogenetic-trees","phylogenetics","protein-domains","protein-families","python","treeview","visualization"],"created_at":"2024-11-18T02:11:11.182Z","updated_at":"2025-05-09T02:21:25.168Z","avatar_url":"https://github.com/LKremer.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"showTree, a visualization tool for gene/protein families.\n=========\n\nshowTree can visualize the following files in a single figure:\n- a multiple sequence alignment (MSA)\n- a gene/protein tree in newick format\n- a protein domain annotation in Pfam_scan output format\n\n\nThe inputs above can be combined freely, e.g. you may provide any combination \nsuch as\n- tree + MSA + domains\n- tree + MSA\n- tree + domains\n- MSA + domains\n- ...\n\n\n\nRequirements\n------------\n\nshowTree requires Python2.7 or Python3.4 or higher and the following Python packages:\n- ete3\n\n`pip install 'ete3==3.0.0b35'`\n- Biopython\n\n`pip install biopython`\n\n\nIt is absolutely crucial that you're using ete3 version 3.0.0b35 and not the latest version. The latest version simply won't work because some\nclasses that showTree depends on were silently removed from ete3.\nThe protein domain annotation must be in the output format of pfam_scan.pl which you can download here: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/ .\n\n\u003cdetails\u003e\n  \u003csummary\u003enote for bornberglab-members who use calcTree (click to expand)\u003c/summary\u003e\nThe input files (MSA and gene tree) may also be computed with calcTree (https://ebbgit.uni-muenster.de/ckeme_01/geneSearch/wikis/calcTree).\nshowTree can also parse the calcTree config file to automatically find the domain annotation of proteins in the MSA.\n\u003c/details\u003e\n\nUsage\n------------\n\n```\nusage: showTree.py [-h] [-m MSA] [-t TREE]\n                   [-d DOMAIN_ANNOTATIONS [DOMAIN_ANNOTATIONS ...]]\n                   [-c CONFIG] [-g GFFS [GFFS ...]] [-o OUTPUT_PATH]\n                   [-s SCALE_FACTOR] [-hl [HIGHLIGHT [HIGHLIGHT ...]]]\n                   [-r ROOT] [-hn HIDE_NODES [HIDE_NODES ...]] [--lineseq]\n\noptional arguments:\n  -h, --help            show this help message and exit\n\nmain arguments:\n  -m MSA, --msa MSA     Path to an untrimmed multiple sequence alignment in\n                        FASTA format (the one produced by calcTree usually\n                        ends with \"_aln.fa\")\n  -t TREE, --tree TREE  Path to a gene tree, i.e. the best-scoring gene tree\n                        with bootstrap values (not as branch labels) produced\n                        by RAxML, usually the file name starts with\n                        \"RAxML_bipartitions.\"\n  -d DOMAIN_ANNOTATIONS [DOMAIN_ANNOTATIONS ...], --domain_annotations DOMAIN_ANNOTATIONS [DOMAIN_ANNOTATIONS ...]\n                        Path(s) to one or more Pfam_scan domain annotation(s)\n                        of the proteins (standard method to display protein\n                        domains)\n  -c CONFIG, --config CONFIG\n                        Path to the geneSearch/calcTree configuration file\n                        (alternative method to display protein domains)\n\nadditional optional arguments:\n  -g GFFS [GFFS ...], --gffs GFFS [GFFS ...]\n                        Path to one or more GFF files containing CDS features\n                        of the proteins. Used to mark intron positions. Only\n                        works if the 9th (=last) column of the GFF contains\n                        the protein IDs\n  -o OUTPUT_PATH, --output_path OUTPUT_PATH\n                        Path to the output image file. Must end with .PDF,\n                        .PNG or .SVG. Tree will be shown in a window if\n                        omitted\n  -s SCALE_FACTOR, --scale_factor SCALE_FACTOR\n                        Horizontal scaling factor of the MSA (default: 1.0).\n                        Decrease this value if your image is too wide!\n  -hl [HIGHLIGHT [HIGHLIGHT ...]], --highlight [HIGHLIGHT [HIGHLIGHT ...]]\n                        Highlight specific clades or terminal nodes with a\n                        background color. Comma-separated IDs will colour each\n                        terminal node separately. Plus-separated IDs will\n                        colour the whole clade that contains those IDs.\n                        Example: --highlight red:prot01,prot02,prot03\n                        green:prot04 lightyellow:prot05+prot06\n  -r ROOT, --root ROOT  Set an outgroup node at which the tree will be rooted.\n                        If multiple IDs are specified (plus-separated), the\n                        whole clade that contains these IDs will be used for\n                        rooting\n  -hn HIDE_NODES [HIDE_NODES ...], --hide_nodes HIDE_NODES [HIDE_NODES ...]\n                        Hide terminal nodes that contain the specified\n                        substring; e.g. use \"FBpp\" to hide all Drosophila\n                        proteins\n  --lineseq             Draw a simple line instead of the amino acid /\n                        nucleotide sequence\n```\n\nExample output\n------------\n\nAn example output tree that was generated with the command\n`showTree -m ORTHO_ALL1421_aln.fa -d ORTHO_ALL1432.pfamscan -t RAxML_bipartitions.ORTHO_ALL1421_aln.tree -s 0.5 -o tree.pdf`\n\n![example_tree](http://i.imgur.com/k52BxkR.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flkremer%2Fshowtree","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flkremer%2Fshowtree","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flkremer%2Fshowtree/lists"}