比较基因组学-比对和建树

makeblastdb -in ref.fa -dbtype prot

blastp -query -db -outfmt 6 -evalue 1e-10 -num_threads 16 -out

muscle -in

mafft --maxiterate 1000 --thread 200 --localpair 

trimal -in cds.fa.muscle -out cds.fa.muscle.trimal -automated1

abyss fa2phy cds.fa.muscle.trimal > cds.fa.muscle.trimal.phy 

iqtree -s cds.fa.muscle.trimal.phy.uniq.fa.phy

 

awk '{print $1}' $1 > $1.tmp

mafft --maxiterate 1000 --localpair $1.tmp > $1.msa
Gblocks $1.msa -b4=4 -b5=a -e=-gb
sed "s/ //g" $1.msa-gb > $1.msa-gb.fa
iqtree -b 1000 -s $1.msa-gb.fa