small, but important fix to rarely used -X parameter that was introduced in release 1.6.20 this is only for when there are more than 1,000 genomes, GToTree automatically uses muscle super5 alignment to help with time required adding this flag prevents GToTree from using the super5 algorithm and sticks with regular muscle alignment algorithm -X wasn't in parsed argument list, so previously if trying to provide it, the run would stop before startin
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
fixing gtt-gen-SCG-HMMs -p parameter; it wasn't being set before and the default 90 was used no matt...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
Now default mode is to use only genes found in single-copy in a given genome, unless "best-hit mode"...
added gtt-cat-alignments to perform concatenation of multiple-sequence alignment files rather than u...
bug fix since addition of gtt-cat-alignments in 1.5.30, needed to adjust how the Partitions.txt file...
adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing ...
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
fix to label swapping when mapping file specified an append only (column 3 present, but column 2 emp...
fix to slight miscalculation of estimated completeness when multiple gene-copies presen
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
fixing gtt-gen-SCG-HMMs -p parameter; it wasn't being set before and the default 90 was used no matt...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
requiring and using muscle5 now thanks to note from @jianshu93 (https://github.com/AstrobioMike/GToT...
Now default mode is to use only genes found in single-copy in a given genome, unless "best-hit mode"...
added gtt-cat-alignments to perform concatenation of multiple-sequence alignment files rather than u...
bug fix since addition of gtt-cat-alignments in 1.5.30, needed to adjust how the Partitions.txt file...
adding in faster alignment settings when working with >= 5000 genomes, and notice about it pointing ...
Cancelling the run immediately and notifying user if -L desired lineage information was provided, bu...
minor bug fix: modifying when gtotree terminates due to an input genome shorter than 100,000 bps to ...
Minor bug fixes; added output file of genes not found in any genome (if any) Codebase: https://githu...
fix to label swapping when mapping file specified an append only (column 3 present, but column 2 emp...
fix to slight miscalculation of estimated completeness when multiple gene-copies presen
genbank and refseq assembly summary tables are now cached instead of downloaded every run (https://g...
updated gtt-genbank-to-AA-seqs to handle those without locus_tags improved gtt-gen-iToL-ma
improvements to working with GTDB (in main script and in gtt-get-accessions-from-GTDB) improvements ...
fixing gtt-gen-SCG-HMMs -p parameter; it wasn't being set before and the default 90 was used no matt...