Version 3.0.0 - Released on December 20, 2023 This release significantly updates the user interface, focusing on making option names more consistent and logical. Additionally some new functionality has been added, and a few bugs fixed. The tables below give an overview of old and new option names for those options that have changed, divided into the 7 argument groups used when printing the command line help. Overview of changes in user-interface Input/Output | Old Option | New Option | Comments | | :------------- | :---------------- | :-------- | | seqconverter [...] SEQFILE | -i SEQFILE | Input file was originally positional argument, but is now specified with -i | | -I FORMAT | --informat FORMAT | Default is to autodetect, so can often be omitted | | -O FORMAT | --outformat FORMAT | Default output format is fasta, so can be omitted in that caseRemoved nexusgap as possible output format - rarely used, and will create new options for gapencoding instead | Selecting subset of sequences | Old Option | New Option | Comments | | :------------- | :---------------- | :-------- | | --subsample N | --sampleseq N | | | --select "REGEXP" | --keepreg "REGEXP" | | | --discard "REGEXP" | --remreg "REGEXP" | | | --subset NAMEFILE | --keepname NAMEFILE | | | --remseqs NAMEFILE | --remname NAMEFILE | | | --filterpos VARIANT[,VARIANT,...] | --keepvar VARIANT [...] | | | --filterdupseq | --remdupseq | In v3.0.0: no longer prints names of removed sequences on stderr | | --filterdupname | --remdupname | | Selecting subset of positions in sequences | Old Option | New Option | Comments | | :------------- | :---------------- | :-------- | | | --samplecols N | New in 3.0.0: Randomly select N columns from alignment | | --subseq START.STOP | --keepcols INDEX_OR_RANGE [...] | Example: --keepcols 10 15 22-40 57 | | --remcols INDEX-LIST | --remcols INDEX_OR_RANGE [...] | Example: --remcols 10 15 22-40 57 | | --remgapcols --remallgapcols --remfracgapcols FRAC | --remgapcols [FRAC] | Covers all variants. If FRAC not given: remove column if any gaps. If FRAC given: remove column if >= FRAC fraction gaps | | --remambigcols | --remambigcols [FRAC] | Now works like the new --remgapcols [FRAC] command. If FRAC not given: remove column if any ambiguity symbols. If FRAC given: remove column if >= FRAC fraction ambiguity symbols | | --remendgapcols FRAC | --remendgapcols [FRAC] | Now works the same way as two options above | | --remhmminsertcols | | Remove option which is rarely used.User can directly use sequencelib if function needed. | Renaming sequences | Old Option name | New Option Name | Comments | | :-------------: | :----------------: | :-------- | | --renamenumber | --renamenum | | | --appendnumber | | Removed rarely used option | | --renameregexp "REGEXP" | --renamereg "OLD_REGEX" "NEW_STRING" | Shortened name.In new version user can provide replacement string (old version always deleted regex) | | --regdupfix | | Removed: now fails with error message indicating duplicate created | | --savenames FILE | --saverename NAMEFILE | | | --restorenames FILE | --renamefile NAMEFILE | | Combining multiple sequence files | Old Option name | New Option Name | Comments | | :-------------: | :----------------: | :-------- | | --overlap--minoverlap N | --overlap [MIN] | Optional value MIN can now be given directly to --overlap | | --mbpartblock | --mb | | DNA manipulations | Old Option name | New Option Name | Comments | | :-------------: | :----------------: | :-------- | | --translate | --translate READING_FRAME | User can now specify in which reading frame to perform translation | Summaries | Old Option name | New Option Name | Comments | | :-------------: | :----------------: | :-------- | | --seqcom | --comseq | | Bug fixes Fixed bug where automatic fileformat detection did not work when input was on stdin Fixed bug where --overlap did not work Fixed bug where --paste did not work