Publication date
August 2020
DOIAbstract
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizing the GTD
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizing the GTD
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
adding small compensation if any white space after accessions in ncbi accessions input file changin...
KO searching finally now fully implemented – only almost a year and a half after @halexand brought i...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
Initial release of GToTree! Codebase: https://github.com/AstrobioMike/GToTree Documentation: https:/...
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
better checking and error message improvement when input accessions file format has problems, and wh...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
adding small compensation if any white space after accessions in ncbi accessions input file changin...
KO searching finally now fully implemented – only almost a year and a half after @halexand brought i...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
Initial release of GToTree! Codebase: https://github.com/AstrobioMike/GToTree Documentation: https:/...
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
better checking and error message improvement when input accessions file format has problems, and wh...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
adding small compensation if any white space after accessions in ncbi accessions input file changin...
KO searching finally now fully implemented – only almost a year and a half after @halexand brought i...
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