{ "info": { "author": "Lars Arvestad", "author_email": "arve@math.su.se", "bugtrack_url": null, "classifiers": [ "License :: OSI Approved :: GNU General Public License v3 (GPLv3)", "Operating System :: OS Independent", "Programming Language :: Python :: 3", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "\n# alv: a command-line alignment viewer\n\nView your DNA or protein multiple-sequence alignments right at your command line. No need to launch a\nGUI!\n\nNote: `alv` requires Python v3.4 or later. Earlier versions may also work, but this has not been\ntested.\n\n### Features\n\n* Command-line based, no GUI, so easy to script viewing of many (typically small) MSAs.\n* Reads alignments in FASTA, Clustal, PHYLIP, NEXUS, and Stockholm formats. \n* Output is formatted to suit your terminal. You can also set the alignment width with option `-w`.\n* Can color alignments of coding DNA by codon's translations to amino acids.\n* Guesses sequence type (DNA/RNA/AA/coding) by default. You can override with option `-t`.\n* Order sequence explicitly, alphabetically, or by sequence similarity.\n* Restrict coloring to where you don't have indels or where there is a lot of conservation.\n\n## Install\n\nRecommended installation is:\n```\npip install --upgrade pip\npip install alv\n```\n\nIf you have a half-modern BioPython installed, Python v3.4 _should_ work. \nBioPython is a dependency and will only get installed automatially with `pip install alv`\nif you are using Python v3.6 or later, because BioPython was apparently not on PyPi before that.\n\n\n## Examples\n\nQuick viewing of a small alignment:\n```\nalv msa.fa\n```\nThis autodetects sequence type (AA, DNA, RNA, coding DNA), colors the sequences, and formats the\nalignment for easy viewing in your terminal.\nWhen applying `alv` to an alignment of coding DNA, the coding property is autodetected and colors are therefore applied to codons instead\nof nucleotides.\n![Seven coding DNA sequences](https://github.com/arvestad/alv/raw/master/doc/screenshot_2.png)\n\n\n\nView three sequences, accessions `a`, `b`, and `c`, from an alignment:\n```\nalv -so a,b,c msa.fa\n```\n\nFeed alignment to `less`, for paging support.\n```\nalv -k msa.fa | less -R\n```\nThe `-k` option ensures that `alv` keeps coloring the alignment (by default, piping\nand redirection removes colors), and the `-R` option instructs `less` to interpret color codes.\n\n## For developers\n\nRun `python setup.py develop test` for development install and to execute tests.\n\n## Screenshots\n\n### Full PFAM domain\n\nAll of the sequences in PFAM's seed alignment for PF00005\n\n![PF00005 seed MSA](https://github.com/arvestad/alv/raw/master/doc/screenshot_PF00005.png)\n\n### Yeast sequences from PF00005\n\nUsing the option `-sm YEAST`, we reduce the alignment to the ones with a matching accession.\n\n![Small MSA from PF00005](https://github.com/arvestad/alv/raw/master/doc/PF00005_yeast.png)\n\n\n\n\n", 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