Estimate branch length with a fixed tree

[lychen83]

Hi Alexis,

I have a data matrix and a phylogenetic tree (I manually changed the topology of a tree obtained from RAxML). It is a Newick tree without branch length. My tree is in this format: ((sagiaginb,sagisagi),sagisubu); I would like to use RAxML to estimate the branch length of the tree with the data matrix. I have used the following command： raxmlHPC-PTHREADS-AVX -s mydatamatrix.fa -m GTRCAT -n seq-GTRCAT -f a -N 200 -k -r mytree.tre -x 1234567 -T 7 The name of the output is 'seq-GTRCAT'. I got a remind: The topologies of all Bootstrap and ML trees will adhere to the bifurcating backbone constraint tree specified in RAxML_bipartitions.ortholog_MO_1005_topology2.tre

The trees in the file 'RAxML_bootstrap.seq-GTRCAT' has branch length, which should be estimated by RAxML. However, the topology of those trees is different from the tree (mytree.tre) I provided. Instead, they are similar to the tree I estimated with my sequences without tree fixation.

Could you help me resolve this problem?

Thank you so much.

Best, Lingyun

[stamatak]

Dear Lingyun,

Could you please re-post this on the RAxML google group?

We will answer it there.

Also please note that standard RAxML is no longer maintained.

We have RAxML-NG now:

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

Alexis

On 17.01.21 13:37, lychen83 wrote:

Hi Alexis,

I have a data matrix and a phylogenetic tree (I manually changed the topology of a tree obtained from RAxML). It is a Newick tree without branch length. My tree is in this format: ((sagiaginb,sagisagi),sagisubu); I would like to use RAxML to estimate the branch length of the tree with the data matrix. I have used the following command： |raxmlHPC-PTHREADS-AVX -s mydatamatrix.fa -m GTRCAT -n seq-GTRCAT -f a -N 200 -k -r mytree.tre -x 1234567 -T 7| The name of the output is 'seq-GTRCAT'. I got a remind: /The topologies of all Bootstrap and ML trees will adhere to the bifurcating backbone constraint tree specified in RAxML_bipartitions.ortholog_MO_1005_topology2.tre/

The trees in the file 'RAxML_bootstrap.seq-GTRCAT' has branch length, which should be estimated by RAxML. However, the topology of those trees is different from the tree (mytree.tre) I provided. Instead, they are similar to the tree I estimated with my sequences without tree fixation.

Could you help me resolve this problem?

Thank you so much.

Best, Lingyun

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-- Alexandros (Alexis) Stamatakis

Research Group Leader, Heidelberg Institute for Theoretical Studies Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology

www.exelixis-lab.org