generate pair wise distance matrix of unrooted phylogenetic tree given by "iqtree"

[Chirag Parsania]

Hi, 

I am quite new to phylogenetic analysis and so IQtree as well. Please bare with me if question does not make sense. 

I am using IQtree to analyse some horizontally transferred genes. I have successfully generated phylogenetic tree using IQtree. I have few questions related to interpretation of the trees given by IQtree.

1). I want to make pairwise comparison of each species given in the tree. To do this, first, I converted unrooted tree to rooted tree using outgroup sequence. Question is, how can I get the pairwise distance of rooted phylogenetic tree ?? I know IQtree gives .mldist file having pairwise distance matrix of final tree given by IQtree. However, I don't know how much the matrix of .mldist file is reliable to use  if I converted original unrooted tree to rooted tree ?? 

Any answer would be highly highly appreciated. 

[Chirag Parsania]

Hi,

I have started same discussion on biostar as well. if anyone would like to answer there. 

[Minh Bui]

Hi Chirag,

Regarding .mldist: Please note that this is not the distance matrix computed from the tree. Instead this is the distance from pairwise sequence comparisons, i.e. just by looking at sequence content — no tree is involved here. The distance is computed using maximum likelihood (that’s why it’s called mldist) based on model parameter estimates from an initial tree. The main purpose of IQ-TREE was to use this distance matrix to build a neighbour-joining tree, which is used as one of the starting trees for more thorough ML tree search.

For the 2nd question, if you want to use a tree to compute the distance (i.e. the path lengths between 2 species), I guess you can use some R package such as APE, though I haven’t use it myself. This should work regardless of rooted or unrooted trees.

Any finally since you mentioned HGT: since this is non-treelike event, you should use some phylogenetic networks such as those implemented in the SplitsTree software.

Hope that helps,

Minh

--
You received this message because you are subscribed to the Google Groups "IQ-TREE" group.
To unsubscribe from this group and stop receiving emails from it, send an email to iqtree+un...@googlegroups.com.
To post to this group, send email to iqt...@googlegroups.com.
Visit this group at https://groups.google.com/group/iqtree.
For more options, visit https://groups.google.com/d/optout.

[Chirag Parsania]

Hi Minh,

Thanks a lot for your reply. It was indeed very useful and important information that .mldist file does not represent the final tree given by IQ-tree. Without knowing that I would have missed tree information. 

I have been using 

cophenetic.phylo

 function implemented in the

ape

package  which converts tree in to distance matrix using branch length. 

One again thanks for your time.