requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToTree/issues/48) using super5 algorithm by default if working with greater than 1,000 genomes, this can be prevented by providing the -X flag added options to gtt-get-accessions-from-GTDB to enable avoiding automatic GTDB database version check, and to store it in the current working directory if wanted (rather than the system variable ${GTDB_dir} setup during conda installation), thanks to feedback from @felixeye (https://github.com/AstrobioMike/GToTree/issues/45
adding -M option to specify number of threads used by muscle, default is 5 (re: https://github.com/A...
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 ...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
small, but important fix to rarely used -X parameter that was introduced in release 1.6.20 this is o...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
removing conda version check from conda-setup.sh script for now Codebase: https://github.com/Astrobi...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
fix for conda version check fix for shell-environment localization variables in conda gtotree enviro...
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
adding -M option to specify number of threads used by muscle, default is 5 (re: https://github.com/A...
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 ...
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
small, but important fix to rarely used -X parameter that was introduced in release 1.6.20 this is o...
can now add lineage info from GTDB if wanted with the -x flag supersedes NCBI lineage info from Taxo...
removing conda version check from conda-setup.sh script for now Codebase: https://github.com/Astrobi...
updating gtt-get-accessions-from-GTDB https://github.com/AstrobioMike/GToTree/commit/bbaec5893342e05...
added comprehensive helper program gtt-get-accessions-from-GTDB to facilitate accessing and utilizin...
fix for conda version check fix for shell-environment localization variables in conda gtotree enviro...
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
fixed missing options/code for subsetting based on arbitrary rank with gtt-subset-GTDB-accessions, r...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
added gtt-gen-SCG-HMMs to be able to generate new SCG-sets the same way those packaged with GToTree ...
adding -M option to specify number of threads used by muscle, default is 5 (re: https://github.com/A...
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 ...