Publication date
August 2020
DOIAbstract
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxonkit if both are provide
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxonkit if both are provide
Initial release of GToTree! Codebase: https://github.com/AstrobioMike/GToTree Documentation: https:/...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
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 ...
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
Initial release of GToTree! Codebase: https://github.com/AstrobioMike/GToTree Documentation: https:/...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
adding gtt-update-ncbi-taxonomy helper script to be able to easily keep the db up-to-date for use wi...
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 ...
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
adding small compensation if any white space after accessions in ncbi accessions input file changin...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
Initial release of GToTree! Codebase: https://github.com/AstrobioMike/GToTree Documentation: https:/...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
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