Is it possible to seqlinkage with a maximum parsimony or minimum evolution method?

3 次查看(过去 30 天)
I try do construct a phylogenetic tree on basis of maximum parsimony (minimum evolution). The function seqlinkage can do this. Method choices are only UPGMA, single-linkage and others, but not the most basic: maximum parsimony. Is there another way to archieve this?

采纳的回答

Luuk van Oosten
Luuk van Oosten 2017-3-10
编辑:Luuk van Oosten 2017-3-10
Dear Anton Huegel,
I am not really familiar with constructing phylogenetic trees in MATLAB, but I believe you could use the function seqneighjoin.
"A neighbor-joining tree can be built using the seqneighjoin function. Neighbor-joining trees use the pairwise distance calculated above [in the example] to construct the tree. This method performs clustering using the minimum evolution method."
So this seems to indicate that the minimum evolution method is in fact included in MATLAB's bioinformatics toolbox...
If this is not sufficient for you: It also seems there is another toolbox available (see also file exchange) made by Cai and co-workers called MBEToolbox, which focuses on sequence data analysis. I had a quick look at it and it seems that maximum parsimony is available there.
Edit: some more on Cai's MBEToolbox: here
  1 个评论
Anton Hügel
Anton Hügel 2017-3-13
编辑:Anton Hügel 2017-3-13
Dear Luuk van Oosten,
thank you very much for your quick response. seqneighjoin will do the trick. And I will totally take a look at the toolbox you mentioned, it seems to have great functionality in this topic.
Thank you very much again, all the best Anton Hügel

请先登录,再进行评论。

更多回答(0 个)

类别

Help CenterFile Exchange 中查找有关 Phylogenetic Analysis 的更多信息

Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!

Translated by