fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, re: https://github.com/AstrobioMike/GToTree/issues/63 also now outputs a GTDB taxonomy table of the subset accession
update to gtdb version file download to coincide with their switch from "VERSION" to "VERSION.txt" (...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
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 ...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
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...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
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" (...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
changed gtt-subset-GTDB-classes to gtt-subset-GTDB-accessions, and incorporated ability to select 1 ...
expanded functionality of gtt-subset-GTDB-accessions to now be able to select 1 random representativ...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
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 ...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
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...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
fixing mistake in summary table reporting which genomes were retained in the final alignment Codebas...
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" (...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
update to gtdb version file download (handled by helper program gtt-check-or-setup-GTDB-files) to co...
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