Unifrac and fungal communities?

08 August 2017 0 8K Report

Hi,

I sequenced ITS3 and ITS4 to study the fungal community of environmental samples. I want to perform an unifrac distance analysis on my samples. However, I failed to align my sequences using muscle. I know that ITS region is variable but the region amplified using ITS3 and ITS4 should be less variable (I found publications in which unifrac was performed starting from DNA fragments amplified using ITS3 and ITS4). Unfortunately, the authors don’t explain the way used to make the alignment. Any idea about which software should I use to perform the alignment?

Thanks

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