I am working on phylogeny of fungi. I amplify IGS1 region but I can not aligned IGS sequences because there are lots of indels. Which programme can I use for aligned and phylogeny? How should I interpret the results ? Help, please..
How did you know if there are indels, when you didn't aligned your sequences. You can align any of the sequence aligners and make a tree. But, if you did sequencing yourself, you have to do quality filtering and analysis with reference database.
Dear Singh
I aligned sequences in MEGA but I saw much indels. I think, another program must be used for IGS. I attached aligned file in the below.
Its not an alignment problem. The alignment looks very good. Its just the sequences, if these are your final sequences, you can proceed to make the tree out of it.
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