Post date: May 15, 2017 5:54:3 PM
Previously, I made trees based on 1000 SNP windows from the whole genomes for the autosomes. All of the individuals sequenced were females, so it seems reasonable to do the same for the Z chromosome, plus this might shed light on its origin.
In the phylo subdirectory,
1. Generate an alignment with just LG23
perl mkLgZ.pl
You have excluded 901292 out of 922532 columns
2. Generate the 1000 SNP trees
perl ../mkRunWindowsZ.pl LycWGSnpAlignment.subLg23 > log
3. In analyses, summarize trees
convert from seq# to id, anna = 0, idas = 1, meliss = 2, sierra = 3, warner = 4
perl -p -i -e 's/seq0/L_anna/g' Zalltrees
perl -p -i -e 's/seq1/L_idas/g' Zalltrees
perl -p -i -e 's/seq2/L_melissa/g' Zalltrees
perl -p -i -e 's/seq3/Sierra_Nevada/g' Zalltrees
perl -p -i -e 's/seq4/Warner_Mts/g' Zalltrees
Run,
Zphylocommands.R
to generate
Zphylo.pdf