I am having trouble processing some alignment data using the packages i normally use (BioEdit and MEGA) and was hoping that others can suggest a better tool to do the following
1) I have a list of 100+ seqeunces from very closely related species which i want to use to look for natural SNP thus suggesting where mutation is least detrimental. What i would like is a tool that i can put these seqeunces in and it can collapse the 100+ seqeunces into groups e.g. group one is 100% identical to my reference, group 2 is 99% identical but has an A to T change at position XXX etc i am thinking this may be similar to RNAseq type work so theres probably a tool in that field which i am unaware of.
2) The list of 100+ sequences includes about 4000bp which have been aligned with ClustalW and now i want to divide it up into segment each containing just one CDS of the operon so i can look at these indivudally - is there a tool which will allow me to select part of an alignment and copy this into a new file