Publication date
February 2020
DOIAbstract
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
updated gtt-hmms to count properly when hmm profile doesn't have accessions in it incorporated exit ...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
better checking and error message improvement when input accessions file format has problems, and wh...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
updated gtt-hmms to count properly when hmm profile doesn't have accessions in it incorporated exit ...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
better checking and error message improvement when input accessions file format has problems, and wh...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
added in check for special characters in user-provided mapping file, re: https://github.com/Astrobio...
updated gtt-hmms to count properly when hmm profile doesn't have accessions in it incorporated exit ...
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