Publication date
March 2020
DOIAbstract
small fix to handle mapping file -m properly when user provides paths to input files in first column rather than just base file name
small fix to handle mapping file -m properly when user provides paths to input files in first column rather than just base file name
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
KO searching finally now fully implemented – only almost a year and a half after @halexand brought i...
adding another step for removal of colons and commas when swapping IDs to make sure they don't end u...
better checking and error message improvement when input accessions file format has problems, and wh...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
fixing a bug where output file final names might be odd if output directory wasn't in current workin...
fix to sloppy integration of "\t" grepping for tabs in while checking input files are formatted prop...
adding final removal of all semi-colons from new labels; prior to this, the user-provided mapping fi...
fix to label swapping when mapping file specified an append only (column 3 present, but column 2 emp...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
bug fix since addition of gtt-cat-alignments in 1.5.30, needed to adjust how the Partitions.txt file...
added capability to start off with amino acid files of coding sequences as input improved handling o...
now generates a partitions file compatible with tree programs capable of using mixed model
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
added gtt-cat-alignments to perform concatenation of multiple-sequence alignment files rather than u...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
KO searching finally now fully implemented – only almost a year and a half after @halexand brought i...
adding another step for removal of colons and commas when swapping IDs to make sure they don't end u...
better checking and error message improvement when input accessions file format has problems, and wh...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
fixing a bug where output file final names might be odd if output directory wasn't in current workin...
fix to sloppy integration of "\t" grepping for tabs in while checking input files are formatted prop...
adding final removal of all semi-colons from new labels; prior to this, the user-provided mapping fi...
fix to label swapping when mapping file specified an append only (column 3 present, but column 2 emp...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
bug fix since addition of gtt-cat-alignments in 1.5.30, needed to adjust how the Partitions.txt file...
added capability to start off with amino acid files of coding sequences as input improved handling o...
now generates a partitions file compatible with tree programs capable of using mixed model
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
added gtt-cat-alignments to perform concatenation of multiple-sequence alignment files rather than u...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
KO searching finally now fully implemented – only almost a year and a half after @halexand brought i...
adding another step for removal of colons and commas when swapping IDs to make sure they don't end u...
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