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ngs-fzb / MTBseq_source

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
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SNP trees #32

Closed peflanag closed 5 years ago

peflanag commented 5 years ago

Hi,

This is more a query than an issue. After running

1) MTBseq --step TBfull 2) MTBseq --step TBjoin .......

I use the .....amended_u95_phylo_w12.plainIDs.fasta file to generate a newick file in FastTree

My query is, is this tree showing SNP differences in the distance between isolates?

Tree

cutpatel commented 5 years ago

No, as you most likely calculated a ml tree. Try a minimum spanning or maximum parsimony tree.

peflanag commented 5 years ago

Cheers. Sorry if this sounds stupid, but can I still use the newick file to make a mini spanning or parsimony tree?

cutpatel commented 5 years ago

No you need the .fasta file alignment and another tool for that. Just google for it.

peflanag commented 5 years ago

Perfect cheers!