How to create a tree with bootstrap?

DessimozLab / read2tree

a tool for inferring species tree from sequencing reads

MIT License

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How to create a tree with bootstrap? #52

Closed sly724 closed 10 months ago

sly724 commented 10 months ago

read2tree --standalone_path marker_genes/ --output_path output --merge_all_mappings --tree

The default tree only has branch length, but no bootstrap. How do I create a tree with bootstrap?

sinamajidian commented 10 months ago

Hi Sly That's true. One of the output of Read2Tree is the MSA: e.g.

 $ head output/concat_merge_aa.phy
 230 133652
sample1 ?????????? ?????????? ?????????? 
sample2 ?????????? ?????????? ?????????? 
sample3 ?????????? ?????????? ?????????? 
...
                         FGELPFHLVR SRRFDDLFEN VLFNYEWLHA
                         FGELPFHLVR SRRFDDLFEN VLFNYEWLHA
                         FGELPFHLVR SRRFDDLFEN VLFNYEWLHA

You can run IQtree on the MSA with ultrafast boostraping using

threads=48
iqtree    -T $threads -s output/concat_merge_aa.phy   -bb 1000

Best regards, Sina

sly724 commented 10 months ago

I get it, thank you very much.

Best wishes, sly