blastdbcmd -db refseq_rna -entry nm_000249  -out test_query.fa

blastn -query test_query.fa -db refseq_rna  -task blastn -dust no -outfmt 7 -num_alignments 2 -num_descriptions 2
 

/apps/muscle/muscle -in /home/mruiz/sequence_ex.txt  -out /home/mruiz/muscle.out | readseq -a -f12 /home/mruiz/muscle.out > /home/mruiz/readseq.out | phyml /home/mruiz/readseq.out 1 i 1 2 JTT 0.0 4 1.0 BIONJ y n