FASconCAT-G offers a wide range of possibilities to edit and concatenate multiple nucleotide, amino acid, and structure sequence alignment files for phylogenetic and population genetic purposes. The main options include sequence renaming, file format conversion, sequence translation, consensus generation of predefined sequence blocks, and RY coding as well as site exclusions in nucleotide sequences. FASconCAT-G implemented process options can be invoked in any combination and performed during a single process run. FASconCAT-G can also read in and handle different file formats (FASTA, CLUSTAL, and PHYLIP) in a single run.
I meant to deal with this 2 years ago after the other minor changes but I got distracted by other projects.
Material changes to code marked with '#jgl#'
cleaned up some formatting
replaced tab characters with 4 whitespaces
script and perl versioning info added to paramters screen and preface as variables
implemented P Kuek change 22nd april to help option
screen clearing that works on macOS, linux and cygwin (check)
attempted to resolve multiple warning, or at least mark them in code, see '#jgl#'
identified info reporting issue [see desription lines 3905-9], but haven't attempted to fix this yet
Please test this version and ensure it's cross compatible with the previous one.
I'm not great with hashes so I wasn't confident about dealing with the info reporting issue,
although I think it's desirable to fix becuase you can get a fairly misleading idea about the the
amount of missing data in your supermatrix if you're not aware of what is actually being reported.
There's also some unintuitive behaviour with the way the -g option works, especially if you have
N|X, -,? characters in a locus file that has less that the total number of sequences in the supermatrix,
whereby the residual sequences that get filled-in following concatenation can then have a distinctly
different makeup to the almost-empty sequneces in the original locus file. -This can be fixed later
Something else to watch out for is pasting code into github issue reponses: the code in some of
your response got severely munged, e.g. the parameter array references got replaced by your
redacted email, etc.
Hi Patrick,
I meant to deal with this 2 years ago after the other minor changes but I got distracted by other projects.
Material changes to code marked with '#jgl#'
Please test this version and ensure it's cross compatible with the previous one. I'm not great with hashes so I wasn't confident about dealing with the info reporting issue, although I think it's desirable to fix becuase you can get a fairly misleading idea about the the amount of missing data in your supermatrix if you're not aware of what is actually being reported.
There's also some unintuitive behaviour with the way the -g option works, especially if you have N|X, -,? characters in a locus file that has less that the total number of sequences in the supermatrix, whereby the residual sequences that get filled-in following concatenation can then have a distinctly different makeup to the almost-empty sequneces in the original locus file. -This can be fixed later
Something else to watch out for is pasting code into github issue reponses: the code in some of your response got severely munged, e.g. the parameter array references got replaced by your redacted email, etc.
Cheers