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Creating a phyloginectic tree from mapped reads which I obtained using bowtie, then IGV.

I am a sophomore who is majoring in biology, and completely new to bioinformatics . I was tasked with searching for Aeromonas in a metagenome. I used bowtie2 to align reads from next-gen sequencing of the metagenome to a FASTA of gryA subunit of two different Aeromonas(ran separate alignments for both). My professor now wants me to create a phylogenetic tree using my results. At the risk of sounding dumb, how do I do this? I created a visual of the alignment using IGV but I'm not sure what software to use to create a phylogeny or even how to go about it in any way.I saw that Mega 7 can create a tree, I've also used Seaview, but how would a create a tree using the files and results I have(Sam,Bam,BAI,) Any help would be greatly appreciated.

alignment genome sequencing
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updated by mks002 mks002 • written by Rustem • Rustem

I know close to nothing about metagenomics, but I know that Kraken is a tool often used and it seems a phylogenetic tree can be constructed using this tool.

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written by WouterDeCoster WouterDeCoster

Thank you WouterDeCoster, genomax2.

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written by Rustem • Rustem

Please use ADD REPLY/ADD COMMENT when replying to existing posts to keep threads logically organized.

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written by GenoMax GenoMax

2 answers

If you have the reads aligned to the gene on interest you could export them from the bam file (bamtofastq). Convert them to fasta format (A: Fastq Convert To Fasta or seqtk ) and then use MEGA7 or any other phylogenetic package to do phylogeny.

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written by GenoMax GenoMax

Just check this out here GraPhlAn tool. For metagenome it gives very nice and detailed images.

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written by mks002 mks002

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