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Sequence Divergence And Phylogenetic Tree

I am trying to generate a phylogenetic tree from the bacterial sequences. I used Jalview program to edit those sequences which are not homologous with the query one (which has 302 AA in length). I cutoff those sequences which have less than 100AA and more than 500 AA in length and then processed to the alignment procedure. I used MUSCLE (in SeaView program) to align the sequences. I used again Jalview to check the 100% similarity of the properly aligned sequences by using redundancy option and then processed the resultant file to create a phylogenetic tree. But, when I tried to create a tree by using NJ method with 100 bootstrap value it says that the sequences are too divergence and couldn't make a tree. I have nearly 500 sequences of bacterial species. Could somebody suggest me to handle this problem? Thanks! -Spandan

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written by spandankeshav • spandankeshav

Maybe you have an input data problem (bad formatting?). As an alternative, maybe one or few sequences screw everything up. You might try and reduce the problem. E.g. start with 25-50 sequences and see if you can build a phylogenetic tree. If it works, then increase the number until you get as close as you can to 500. Also, probably you have some indication on outlier sequences, i.e. those that align less to all the other. Try and remove them.

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written by Fabio Marroni Fabio Marroni

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