Right Now I'm currently trying to put 12 whole genomes into a phylogenetic tree. The Genomes were mapped from a reference and they've been converted a couple times (i.e. Bam to Sam, Sam to Fastq, Fastq to fasta), but they look great(we uploaded one to Genious to check if everything was in order). I'm working with FastTree and I'm trying to create a tree with these fasta files, but every time I try uploading one of the genomes, the program will run for a while, but it won't actually do anything. The output tree files are blank and nothing's going into them. The command I'm using is
./FastTree -nt Filename.fasta > myTree
I've seen a similar thread, and I made sure to check that I'm calling the program and that is downloaded and that I'm calling the right files, but i'm still getting a blank file. Any suggestions would be appreciated.