| add Python version of DAGchainer to get collinear anchors |
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almost 13 years ago
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| Merge branch 'master' of github.com:tanghaibao/jcvi |
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almost 13 years ago
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| add apps.phylo to build trees of homeologous gene groups |
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almost 13 years ago
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| add algorithms.catalog.layout() to format OMG ortholog list to columns |
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almost 13 years ago
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| add algorithms.catalog.omgparse() to extract gene lists from OMG outputs |
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almost 13 years ago
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| add algorithms.catalog.omg() for wrapping OMG (started but not finished) |
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almost 13 years ago
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| added `--pasa` options to gff.format() to chain together child features into parent for gff files generated by PASA. Added hack to workaround urlparse.parse_qsl() behavior of replacing '+' symbols with ' '. Added new `btab` dialect to parse 'aat_aa' output files and convert to gff3 format. |
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almost 13 years ago
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| add option for MUSCLE in apps.ks |
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almost 13 years ago
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| use --dist=20 as default for algorithms.synteny.scan() |
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almost 13 years ago
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| allow arbitrary track placement in graphics.karyotype |
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almost 13 years ago
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| allow automatically inference of --qbed and --sbed based on filename |
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almost 13 years ago
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| add genome dups in algorithms.paper.amborella() |
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almost 13 years ago
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| Moved assembly.cap3 to `apps`. Minor update to README.rst |
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almost 13 years ago
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| add jcvi.formats.psl to parse psl files. allows conversion to gff3 format. implemented pct_id and score calculations based on ucsc blat faq (http://genome.ucsc.edu/FAQ/FAQblat#blat4) |
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almost 13 years ago
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| add algorithms.synteny.spa to generate ordering for plotting karyotypes |
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almost 13 years ago
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| add option --canonical to formats.fasta.clean() to remove non-ACGTN chars |
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almost 13 years ago
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| add assembly.patch.pastegenes() |
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almost 13 years ago
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| report "Missing" category in assembly.patch.paste() |
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almost 13 years ago
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| add algorithms.catalog and move algorithms.tandem inside it |
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almost 13 years ago
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| allow algorithms.synteny.liftover to also correct scores in anchorsfile |
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almost 13 years ago
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| restore ostrip behavior and fix some bugs |
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almost 13 years ago
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| fix bug (minor) |
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almost 13 years ago
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| fix formatting bugs (minor) |
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almost 13 years ago
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| wrap plt.savefig inside a base function savefig to handle tex errors |
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almost 13 years ago
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| fix algorithms.synteny.mcscan inefficient use of seen |
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almost 13 years ago
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| change "-num_alignments" to "-max_target_seqs"; add support for Allpaths K-mer histogram |
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almost 13 years ago
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| add non-self option in algorithms.tandem; add --mergetandem in algorithms.synteny.mcscan() |
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almost 13 years ago
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| Fixed formats.gff.split() which was affected by commit 1ae18f4 (contig id is now being accepted as a named parameter `--contigs`) |
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almost 13 years ago
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| Fixed typo! |
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almost 13 years ago
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| Modified AHRD template to now alter score_weight parameters based on the BLAST program being run (blastp or blastx). Also added new commandline option to specify blast program. |
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almost 13 years ago
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