Assemble reads for a specific gene I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species are too divergent, reads will not match and I won't get the full CDS. Is there a better way to deal with that? Maybe I can do that to retrieve the well conserved part and then extend this region with reads that overlap (as if it was gap-filling)? 
What do you think of this approach? Do you know a software for such extension process? 
Thanks
That's a good question. I remember seeing a poster about making trees directly from reads, but unfortunately, I can not find any other record than this tweet. Perhaps you can try to email David, if he would be keen to share the implementation. 

While searching for any information about David's work, I run into a GitHub repository called reads2trees. It's quite old and it's not super popular, so hard to say if it can be useful. But the name matches the problem description quite well.

I also remember there were some attempts (An example paper) to get phylogeny directly from kmers, but I have never tried that on my own. I also think these approached were focused on microbial phylogienies. So again, not sure if it's going to be useful for you.

That's all I got.