how to use fasttree to analysis hundreds of sequences？

Question

[xiaozhan063]

hi, everyone

i want to align hundreds of sequences,from the other posts this forum, i choose the software fasttree to construct the phylogenetic tree. and when i entered in C (language), what orders should i fill in? and i tried to fill in the orders as the illustration of the software, but there was no respond?

Answer 1

[5heikki]

I have no idea what you mean by "entered in C" but e.g. FastTree protein_alignment > tree will make a tree.

[xiaozhan063]

I feel very sorry for my grammar mistakes, "entered in C" represent that I use C programming as the illustration of the software. FastTree protein_alignment > tree I want ask you that the protein_alignment is the protein sequences fasta format file? Or only mean the word protein_alignment?

[xiaozhan063]

First step, open the fasttree.exe

Second, I fill the order as you showed

There is no respond of the program. And what can I do with this situation? Correct me if I'm wrong, thank you!

[5heikki]

FastTree proteinAlignment.fasta > ProteinAlignment.tree

The proteinAlignment.fasta file should come from some MSA program like e.g. muscle. The resulting .tree file you can open with e.g. FigTree, but really I don't know what's available for Windows. People who do bioinfo related tasks with Windows are a few. Also, you're doing tasks from the command line. This has nothing to do with C..

[xiaozhan063]

Thank you for your attention, form the Fasttree software website, the most suitable version is not windows system, but it also stated that the windows system can open the fasttree via C programe, and I have written the order as you shew (the fasta was saved by the MegAlign),but the result as the second chart which attached before. All in all, I will keep trying the fasttree software. Thank you very much.

Last, I want ask you the other question, I have selected dozens of typical sequences, and align them with the MEGA software, and I have some questions about the phylogenetic tree ,one is that the value of the bootstrape were very low， and in some branch the value is zero, but these sequences in the MegAlign, the identify of these sequences is all above 85%. and why is this happening?

[xiaozhan063]

Thank you for your attention, I have learned to use the fasttree software in DOS, but a new problem has arisen, when the sequences length are differ, the program would shown wrong in some short sequences, and what should i do next?