FastTree running problem

Question

[horsedog]

Hi all, I'm using FastTree Version 2.1.10 SSE3 to do the phylogenetic analysis. But here I ran into a problem, it keeps giving me the error :

Amino acid distances: BLOSUM45 Joins: balanced Support: SH-like 1000 Search: Normal +NNI +SPR (2 rounds range 10) +ML-NNI opt-each=1 TopHits: 1.00*sqrtN close=default refresh=0.80 ML Model: Jones-Taylor-Thorton, CAT approximation with 20 rate categories Ignored unknown character X (seen 3 times) Segmentation fault: 11

My file is big amino acids file, with more than 1000 sequence , 500 bps. I tried to put in

FastTree -out tree amino_rename.fasta;

FastTree amino_rename.fasta > tree;

FastTree -wag amino_rename.fasta > tree;

no one works, does anybody have idea?

Answer 1

[h.mon]

X is code for an unknown aminoacid at that position, and apparently FastTree doesn't like X. Remove the sequences which have X and try again.