Find divergent sites in conserved sequences
$ perl conDivFinder.pl -in <input.fasta> -l <species.list> -w <window size> -con <conserved number> -div <changed number> -bn <background can not conserved species>
-in input.fasta : sequence aligned in fasta format file
-l species.list : species list with species marked
-w window size : default 20 , the window size for calculating the conserved region
-con conserved number : default 18 , identify as conserved region if the number of nucleotides in the window is large or equal to this value
-div changed number : default 12 , identify as changed region if the number of nucleotides in the window is less or equal to this value
-bn background can not conserved species : default 0 , how many species can not be conserved in the background species
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species list file format, one species per line and foreground species marked with '*':
human
mouse
snake *
frog
caecilian *
...
fasta file format: # species name should not contain '.' '-' '@' etc. ; '_' is allowed ; the first species should be the reference species
>species_name
AAGCTTGGG
or
>species_name.seqId
AAGCTTGGG