Q&A added during the Basic bioinformatics training

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Please find here questions raised during the sessions


Multiple sequence alignment

Which alignment tools to use ?

As an alignment editor MEGA is a good choice, to make alignments Muscle and MAFFT are good options. Try both and compare the results. For extremely large data sets use Clustal Omega.

How to combine alignments of multiple genes into one tree ?

To combine alignment of multiple genes into a tree see this review paper.

There are two methods to combine multiple genes into a tree:

  • gene sequences are concatenated into a super-gene alignment, which is then analyzed to generate the species tree
  • phylogenies are inferred separately from each gene, and a consensus of these gene phylogenies is used to represent the species tree
There’s a lot of discussion on which is the best.

Practically, you can do concatenation in MEGA and construct the tree in MrBayes or PAUP: e.g. align each gene separately with Muscle in MEGA and save the alignment of each gene. Then, import the alignment file of each gene using the "Analyze" button and transform to "meg" format. At last, concatenate each gene matrix together. There’s software to do the concatenation e.g. Sequence Matrix.

On prokaryotes the results of concatenation are not so good: see paper.