software: MEGA X, for ex: total 66 genes(protein sequence) of same species taken for the study, at the step of alignment(ClustalW) it is showing that " sequence is mor divergent : abort or ignore" if i will click abort that sequence is not aligning and incase of clicking ignore: only few sequences are getting align like 33 sequences only aligned and i need to align all 66 sequences. how overcome this issue ??
There are dozens of good multiple sequence alignment programs (MAFFT, Muscle, T-Coffee, etc.) there is no reason to limit yourself to CLUSTALW. Most software wants the sequences in FASTA format (it's a plain ASCII text format, nothing fancy) and you can import and export FASTA format files from most packages such as MEGA. But if the sequences are not clearly well aligned by a program such as MAFFT or CLUSTALW, they may be too distant for good phylogenetic analyses anyway. Always look at the alignment in an alignment viewer/editor such as AliView or BioEdit (they are both free) before moving into the analyses.
Sir, thanks for u r suggestions I will try another software for alignment and tried with clustalW Phylogeny tree is too distant for analyses.
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