Hello everyone,
I´m trying to develope a phylogenetic tree for a novel species. I already have many MSA but I cant find anything on how to trim such ones. For example from which sequence to which sequence is the best way or something like that.
Hopefully someone has an advice for me.
Thanks,
Philipp
NO. There is no standard over how to trim an alignment. You could have asked , is it logical to trim an alignment? And the answer is debated and there is not congruence over whether to trim or not to trim.
But if you want to trim an alignment, you can try TrimAl or Gblocks.
You can use BioEdit for trimming/visualizing/correcting the aligned sequences.
trimal is a tool which is useful for automated removal http://trimal.cgenomics.org/
However, if you are looking for manual removal then it requires visual judgement and experience!
There is no standard measures saying to what extent we can trim our sequence. But, deleting up to first 50 bases from both ends will increase the quality of sequence. This is because their base strength is very less to be included in analysis part. However, the process of trimming limit is mainly depends on bringing homogeneity among all our analyzing sequences.
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