I am a beginner user of Galaxy, and I am trying to do a phylogenetic analysis of a fungal species. I have about 85 sequences for multiple-sequence alignment using MAFFT. It has been more than 24 hours, and the process is still not complete. I want to know if there is a way to check the progress of the alignment process.
as another option, you may consider using protein sequences from orthologous genes, if the genomes are annotated.
How do you prepare the input file for MAFFT job, by concatenation of genomes? If your fungal species have multiple chromosomes, you can terminate the job. Both MAFFT and ClustalW align every sequence to other sequences. Usually there is very little similarity between chromosomes in a genome.