Publication date
April 2020
DOIAbstract
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use with taxonki
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use with taxonki
minor bug fixes; additional output report added Codebase: https://github.com/AstrobioMike/GToTree ...
fixing version disparity because i can never remember to update it with changes before release – i k...
better checking and error message improvement when input accessions file format has problems, and wh...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
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...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
initial addition of iqtree, basic use right now (not yet doing partial models automatically) Codeba...
minor bug fixes Codebase: https://github.com/AstrobioMike/GToTree Documentation: https://github.co...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
minor bug fixes; additional output report added Codebase: https://github.com/AstrobioMike/GToTree ...
fixing version disparity because i can never remember to update it with changes before release – i k...
better checking and error message improvement when input accessions file format has problems, and wh...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
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...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
initial addition of iqtree, basic use right now (not yet doing partial models automatically) Codeba...
minor bug fixes Codebase: https://github.com/AstrobioMike/GToTree Documentation: https://github.co...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
minor bug fixes; additional output report added Codebase: https://github.com/AstrobioMike/GToTree ...
fixing version disparity because i can never remember to update it with changes before release – i k...
better checking and error message improvement when input accessions file format has problems, and wh...
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