I want to align all the orthologous genes of some genomes, so i could obtain the genome tree.
I had generated the fasta files, each file contained all the genes of one genome.
I used BLAST for each pair of genomes, and generated the lists.
From each genome I selected one gene, s.t. each gene was the best hit of the other genes.
But I obtained only less than 20 orthologous genes with just 3 genomes,
while more than 1000 genes were obtained with 2 genomes.
When more genomes was included, almost no orthologs could be found.....
Any one have efficient methods? Is the method I used too strict?
btw, this is the option I used for blastn :
-task blastn -> I tried blastn-short, but the result was somehow worst
-evalue 5 -> not sure what value to be
-max_target_seqs 5 -> when larger, or not to set this option, I got a little more orthologs ...... why?