Question: How to do a phylogenetic tree?
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gravatar for javisbs
4 weeks ago by
javisbs0
javisbs0 wrote:

Hello. I need to do a phylogenetic tree of 5 diferent species. I did one in MEGA for the proteins but now I need to do it for the entire genomes for the end of degree project. The genomes are fragmented in some contigs. I can´t do it in MEGA cause they are fragmented so I searched omic tools and I found JSpeciesWS but this program doesn´t give me the phylogenetic tree, it gives me the % of similarity. Is there any page or program for do a phylogenetic tree from the percent of similarity or from the genomes sequences with the different contigs? I can use R and Python too

assembly genome • 194 views
ADD COMMENTlink written 4 weeks ago by javisbs0

Hello, I am not sure but biopython maybe helpful for you.

ADD REPLYlink written 4 weeks ago by MatthewP60

phylogenetic tree from contigs - this is your question

What 5 diferent species do you study? Since it was not clear,

I found at least something in Biostars:

See these posts and links:

For bacteria:

What Next After Contigs?

for others:

MSA and Phylogeny after De-Novo-Assembly

to assemble the genome:

Genome assembly from contigs assembled by WGS

Mash: fast genome and metagenome distance estimation using MinHash

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4915045/

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by natasha.sernova3.3k

Creating a tree from an entire genome is not straightforward as you cannot align that much sequence in a meaningful way.

What you might be interested in though, are mash distances. You can create trees using mash distances as a surrogate for ANI, but its capable of working at that scale.

See: https://github.com/lskatz/mashtree

ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by jrj.healey10k
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