run ML search indepedently after rapid bootstrapping

[dv]

Hi all,

I ran  the following command for constructing the tree after bootstraps and ML search

raxmlHPC -f a -x 45689 -p 12358 -# 100 -m PROTCATLGF -s /DATA/dea/deavincent/raxml_run_for_entire_dataset_21oct/tree_input_4180+10_archea_copy_concatenated.aln -n entire_dataset1 -o GCF_000013445.1_ASM1344v1,GCF_000186365.1_ASM18636v1,GCF_000204415.1_ASM20441v1,GCF_002078355.1_ASM207835v1,GCF_002156965.1_ASM215696v1,GCF_002813695.1_ASM281369v1,GCF_003201835.2_ASM320183v2,GCF_004799605.1_ASM479960v1,GCF_900012635.1_Pyrococcus_chitonophagus_genome_sequence,GCF_900090055.1_C.divulgatum_PM4 -T 24

after the run was completed i realized this command only gives me the bootstrapped trees without branchlengths. Now i want to run ml search on this and get a final output that would be equivalent to running

raxmlHPC -f a -m GTRGAMMA -p 12345 -x 12345 -# 100 -s dna.phy -n T20

is there a way to do that

[Alexandros Stamatakis]

Please not that standard RAxML is not supported any more, you might
consider switching to RAxML-NG

https://github.com/amkozlov/raxml-ng

Please have a look at:

https://cme.h-its.org/exelixis/web/software/raxml/hands_on.html

for a step by step tutorial.

You can indeed infer a couple of ML trees with standard RAxML and then
invoke RAxML once more to draw the support values from the BS trees onto
the best found ML tree or use another raxml invocation to compute a
consensus tree from the BS trees.

Alexis

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--
Alexandros (Alexis) Stamatakis

ERA Chair, Institute of Computer Science, Foundation for Research and
Technology - Hellas
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.biocomp.gr (Crete lab)
www.exelixis-lab.org (Heidelberg lab)