Creating Phylogenetic tree from MAF format file

mez · 08-29-2012, 07:40 AM

I hope this is relevant to the discussions here.

I am working on a metagenome project and have genome sequences of several strains of a bacteria species, un-assembled, but in contig reads. I used the mugsy program to align them and I have been trying to find a tool to create a tree out of the MAF format file I generated, but I am having issues because of the nature of the original sequences being in contigs rather than assembled.

I am hoping someone jas worked with unassembled genomes with contig reads and could be able to point me to how I could generate an acceptable multi-alignment format from the data

Thanks as always.

mez.

themerlin · 08-29-2012, 12:37 PM

I'm a little unclear about your question. If you have contigs, then you are working with an assembly. Do you mean that you are working with overlapping paired-end reads?

mez · 08-31-2012, 01:12 PM

Sorry, I guess I should say the reads have been assembled into contigs, I was having trouble aligning the genomes of the different strains, but I am making progress on that now. Just trying to figure how best to use the MAF format file generated to create a phylogenetic tree.

themerlin · 09-04-2012, 10:02 AM

I'm not sure that you can create a tree from a MAF file with overlapping reads. With Mugsy, you usually provide separate files for each genome and then infer a tree from sequence conserved in each block. If you can get your MAF file in this format, you can create a FASTA alignment with Galaxy or with scripts in the bx-python package (https://bitbucket.org/james_taylor/bx-python/wiki/Home).

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08-29-2012, 07:40 AM	#1
mez Junior Member Location: georgia Join Date: Nov 2011 Posts: 5	Creating Phylogenetic tree from MAF format file I hope this is relevant to the discussions here. I am working on a metagenome project and have genome sequences of several strains of a bacteria species, un-assembled, but in contig reads. I used the mugsy program to align them and I have been trying to find a tool to create a tree out of the MAF format file I generated, but I am having issues because of the nature of the original sequences being in contigs rather than assembled. I am hoping someone jas worked with unassembled genomes with contig reads and could be able to point me to how I could generate an acceptable multi-alignment format from the data Thanks as always. mez.

08-29-2012, 12:37 PM	#2
themerlin Member Location: Flagstaff, AZ Join Date: Feb 2010 Posts: 51	I'm a little unclear about your question. If you have contigs, then you are working with an assembly. Do you mean that you are working with overlapping paired-end reads?

08-31-2012, 01:12 PM	#3
mez Junior Member Location: georgia Join Date: Nov 2011 Posts: 5	Sorry, I guess I should say the reads have been assembled into contigs, I was having trouble aligning the genomes of the different strains, but I am making progress on that now. Just trying to figure how best to use the MAF format file generated to create a phylogenetic tree.

09-04-2012, 10:02 AM	#4
themerlin Member Location: Flagstaff, AZ Join Date: Feb 2010 Posts: 51	I'm not sure that you can create a tree from a MAF file with overlapping reads. With Mugsy, you usually provide separate files for each genome and then infer a tree from sequence conserved in each block. If you can get your MAF file in this format, you can create a FASTA alignment with Galaxy or with scripts in the bx-python package (https://bitbucket.org/james_taylor/bx-python/wiki/Home).