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 case<br>Removed nexusgap as possible output format - rarely used,<br> 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<br> VARIANT[,VARIANT,...] | --keepvar VARIANT [...] | | | --filterdupseq | --remdupseq | In v3.0.0: no longer prints names of removed sequences on stderr <tr></tr> | | --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<br> --remallgapcols<br> --remfracgapcols FRAC | --remgapcols [FRAC] | Covers all variants. <br>If FRAC not given: remove column if any gaps. <br>If FRAC given: remove column if >= FRAC fraction gaps | | --remambigcols | --remambigcols [FRAC] | Now works like the new --remgapcols [FRAC] command.<br> If FRAC not given: remove column if any ambiguity symbols. <br>If FRAC given: remove column if >= FRAC fraction <br>ambiguity symbols | | --remendgapcols FRAC | --remendgapcols [FRAC] | Now works the same way as two options above | | --remhmminsertcols | | Remove option which is rarely used.<br>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 <br>"OLD_REGEX" "NEW_STRING" | Shortened name.<br>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<br>--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<br> 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