Scripts

The script can convert FASTA sequences into other file format (.phy/nex/rdf, etc),

concatenate sequences that have the same ids, select codon sites, etc.

The script digests FASTA with MseI and EcoRI (digest.fas),

then fragments were selected based on sequences of both ends (SelectivePCR.fas).

The script picks sequences with a length (+/- range) from multiline fasta library and summarizes into "outseq.fas".

The script converts GENEPOP (.txt) into a BEAST v1 text file.

The script converts Fasta files into a DIYABC infile. Files for each population and locus (and each phase for autosomal nuclear locus) are required.

The program detects SNPs that are fixed in the populations.

Two Fasta files for the population#1 (foreground) and the population #2 (background) are then compared and SNPs are listed in text file.

R scripts

<GRID.AREA.R>

The script is written for obtaining a fraction of depth layers in marine regions and used in the following paper:

Sakuma K, Fujiwara K, Ueda Y, Yoshikawa A, Yosho I (2018)

Regional variation in size of sexual transition of the commercially important protandric hermaphrodite northern shrimp Pandalus eous in the Sea of Japan. Submitted.

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