How to build a phylogenetic tree

1. make alignment

2. trim alignment
   trimal
   trimal -in aligned_seq.fasta -out name.trimal.fasta -gt 0.3 -st 0.001

3. Fast Tree
4. RAxML

basic command for ML tree on nucleotide sequences with fast bootstrap

raxmlHPC-PTHREADS-SSE3 -T 4 -m GTRCAT -c 25 -e 0.001 -p 31415 -f a -N 100 -x 02938 -n name -s name.aln.fas

1. IQtree
2. PhyloBayes

How to view a phylogenetic tree

1. FigTree In case it is not running, you can try experimental version.