Constructing a phylogenetic tree of a gene family with over 400 sequences

Question

[star_143_101]

I have 414 sequences of LRR gene family from tobacco.I want to construct a phylogenetic tree using MEGA 6.but it gives an erroe but if I try 100/100 sequences one by one it gives no error.so I thought may be due to the high number. I have no experience with such a large number of sequences. What should I do now - please guide me?

Answer 1

[Daniel]

I would recommend generating the alignment using the actual algorithm that you want to use, then import the alignment back into MEGA for doing the tree.

If you don't have a machine powerful enough, try out somewhere like: https://www.ebi.ac.uk/Tools/msa/muscle.

Also note that trying to present so many sequences in a tree might be hard to interpret. I used to use http://topiaryexplorer.sourceforge.net/, but it might be out dated now.

Answer 2

[zeeefa]

I'd suggest you to use the CIPRES portal for phylogenetics analysis :) it doesn't have MEGA though.