Creating A Phylogenetic Tree From A Multiple Sequence Alignment.

Question

[shiheng0828]

My teacher told me that I can create a phylogenetic tree from a multiple sequence alignment by using TreeBeST.

I tried several times but I failed. I am not sure what cause the problem.

I am a beginner in Bioinformatics.

What's worse is that this project should be finished soon.

Hope someone can help me.

Firstly, according the TreeSoft: TreeBeST, I downloaded the treebest-1.9.2_i386-win32 from the following link: https://sourceforge.net/projects/treesoft/files/treebest/1.9.2/.

Secondly, prepare multiple alignment named aligned.fasta file, which is from step 1.

aligned.fasta:

>sp|1
-------ACCAACGTCTACCAGATTCACGAGCCGTCC
>sp|2
GGGGATGGTCGATGTCCGGCGGG-----GTGCCTT--
>sp|3
TCATATGCCAAATTTCTCCACGT-----GGGACGG--

Finally, use cmd in windows.

C:\Program Files\Alignments\treebest-1.9.2_i386-win32>treebest best aligned.fasta > out.tree.nhx
Results:
[best_core] less than 3 sequences. PHYML is skipped.
[ma_trans_align] not seem to be a nucleotide alignment (37).
[ma_nucl_filter] fail to translate a nucleotide alignment. Filtering abort.
[ma_trans_align] not seem to be a nucleotide alignment (37).
<best_core> fail to translate the alignment. Is it a valid coding alignment?

C:\Program Files\Alignments\treebest-1.9.2_i386-win32>

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[Vitis]

Based on the error message, it seems the input is not right. From the lines you posted, it doesn't look like in FASTA format. Is this some kind of homework? If so, this would be a good opportunity to read through TreeBeST documentation and figure this out.

[Ram]

True. This is gapped fasta, and the tool should allow for gapped fasta input or this file won't work. Also, given that the sequences are 36 nucleotides long, and the tool is encountering a invalid character error, plus the fact that you're working on Windows, can you check and make sure the line endings are proper? Maybe convert \r\ns to \ns and try the command again?

[shiheng0828]

Thank you for your reply.
My system is windows, but the fasta file ends with \n. It seems TreeBest needs the input 'AAA' or '---'. aligned.fasta

>sp|1
-------ACCAACGTCTACCAGATTCACGAGCCGTCC
>sp|2
GGGGATGGTCGATGTCCGGCGGG-----GTGCCTT--
>sp|3
TCATATGCCAAATTTCTCCACGT-----GGGACGG--`

The aligned.fasta is gotten by using muscle3.8.31_i86win32.exe. The original sequence does not have gaps. I use muscle3.8.31_i86win32.exe to convert sequences into multiple alignment, aligned.fasta.

In fact, the purpose of the project is to design and implement a program for constructing ancestral sequences to the internal nodes of phylogeny, from phylogeny and sequences to the leaves of the tree.

My teacher separated the project into three steps.

Step 1: convert sequences into multiple alignment (Tech)
Step 2: get phylogenetic tree from multiple alignment (Tech)
Step 3: According to the multiple alignment and phylogenetic tree, create ancestral sequences.

Now, I got problem in the step2.

[Ram]

Can you try changing the line endings to \r\n? Also,please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.