I'm doing a project on evolutionary relationship and pathway reconstruction of anthocyanin pathway on solanaceae family plants. I collected 13 group of gene sequences (850 seqs.) It was difficult to align multiple sequences because of the large number of sequences.
How can I prepare the Multiple Sequence Alignment for phyogen. tree construction? I got error when using MUSCLE in mega software and in clustalw I got a result but there are many columns of aligned sequences... how do I align them manually? How do I select columns for phylogenetic tree construction? Thank you.
Try this for evolutionary relationship
http://www.ebi.ac.uk/goldman-srv/webprank/
or
http://www.ebi.ac.uk/Tools/msa/
If your final goal is to build a phylogenetic tree, you must reduce the amount of taxa numbers because although you succeed to calculate tree, it will be difficult to draw a tree. About the multiple sequence alignment, you must use Linux-based clustalw or other programs instead of Windows-based beause of the memory probelm. And if possible, use the queuing system to perform your calculating job in batch condition. Some times, multiple sequence alignment takes several days.
If you use fasta sequence then in allignment sectio, you can edit your sequences and there a a dialogue box come appears, where you can choose sequences you want to align
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