pegi3s/fasttree
FastTree (http://www.microbesonline.org/fasttree) docker image.
608
You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/fasttree bash -c "FastTree -nt -gtr -gamma /data/input > /data/output"
In this command, you should replace:
/your/data/dir
to point to the directory that contains the FASTA file you want to analyze.input
to the actual name of your input file.output
to the actual name of your output file.To see the FastTree help, just run docker run --rm pegi3s/fasttree FastTree -help
.
To test the previous command, you can copy and paste the following sample data, which consists of aligned sequences obtained from here, into the input
file:
>AF264073.1 Drosophila capricorni alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGTATTGATAATCCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACCTTCTTCCCCTACGATGTGACCACATCCTTGGCCGAGACCTCCAAATTGCTGAAAACCAT
TTTCGCTCAACTGAAGACTGTCGATGTTCTGATCAATGGAGCTGGCATTCTGGACGATCATCAGATTGAA
CGCACCATTGCCGTCAATTTCACCGGCCTGGTCAATACCACAACCGCAATTTTGGACTTCTGGGACAAGC
GTAAGGGTGGTCCAGGTGGTGTGATCTGCAACATTGGATCGGTGACTGGTTTCAATGCCATCTACCAGGT
GCCCGTCTACTCGGCATCGAAGGCAGCTGTCGTCAGCTTCACTCAGTCCATTGCC
>AF264074.1 Drosophila equinoxialis alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTGGATCGTATTGACAATCCTGCTGCCATCGCTGAACTGAAGGCAATCAATCCCAAAG
TAACAGTTACTTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTTCTAATCAATGGAGCTGGTATTTTGGATGATCATCAGATTGAG
CGAACCATTGCCGTGAACTTCACTGGTTTGGTCAATACCACCACAGCTATTTTGGACTTCTGGGATAAGC
GCAAGGGTGGACCAGGTGGTGTCATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTATCAGGT
CCCTGTCTATTCTGCATCAAAAGCACGTGTTGTTAGCTTCACTCAATCCATTGCC
>AF264075.1 Drosophila fumipennis alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGGTCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACCTTCTATCCCTATGATGTGACCGTACCCTTGGCGGAGACCACCAAATTGCTAAAGACCAT
TTTCGATCAACTCAAGACTGTCGATGTTCTGATCAATGGTGCTGGCATTCTAGATGATCATCAGATCGAG
CGTACCATTGCTGTGAAATTCACTGGTCTGGTCAATACTACAACGGCCATTCTGGACTTCTGGAACAAGC
GTAAGGGTGGTCCAGGTGGTGTGATCTGCAATATTGGCTCGGTGACTGGTTTTAATGCCATCTACCAGGT
GCCTGTCTATAGTGCATCAAAGGAGGATGTTGTTAGCTTCACTCAATGTATTGCC
>AF264076.1 Drosophila insularis alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGGTCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACTTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACCACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACCGTCGATGTTCTGATCAATGGAGCTGGCATTTTGGATGACCATCAGATTGAG
CGCACCATTGCTGTGAATTTCACTGGTCTGGTCAATACCACGACAGCCATTTTGGACTTCTGGGACAAGC
GTAAGGGTGGTCCAGGTGGTGTCATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTATCAGGT
GCCTGTCTATAGTGCATCAAAGGAGGATGTTGTTAGCTTCACTCAATGTATTGCC
>AF264077.1 Drosophila nebulosa alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGCATTGACAAGCCTGCTGCCATGGCGGAACTGAAGGCAATCAATCCCAAAG
TGATAGTTACCTTCTATCCCTATGATGTTACCACACCCATTACGGAGACCACCAAATTGCTAAAGACCAT
TTTCGCTCAACTAAAGACCGTTGATGTGCTGATCAATGGTGCTGGCATTTTGGATGATCATCAGATTGAG
CGCACCATTGCCGTTAACTTTACTGGTTTGGTTAATACCACCACGGCCATTTTGGACTTCTGGGACAAGC
GTAAGGGTGGTCCAGGTGGTGTTATTTGCAACATTGGTTCGGTGACTGGCTTCAATGCCATTTACCAAGT
GCCCGTCTATTCCGGCATCGAGGCAGCAGTTGTTAGCTTCACTCAATCGATTGCC
>AF264078.1 Drosophila paulistorum alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGCATTGACAAGCCTGCTGCCATGGCGGAACTGAAGGCAATCAATCCCAAAG
TGATAGTTACTTTCTATCCCTATGATGTGACCACACCCTTGACAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTTCTGATCAATGGAGCTGGCATTTTGGATGATCATCAGATTGAG
CGAACCATTGCCGTGAACTTCACTGGTTTGGTCAAAACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GTAAGGGTGGACCAGGTGGTATTATCTGCAACATAGGATCGGTGACTGGTTTCAATGCCATGTACCAGGT
CCCCGTCTACTCGGCATCGAAAGCAGCTGTCGTCAGCTTCACTCAGTCCATTGCC
>AF264079.1 Drosophila pavlovskiana alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAACTGAAGGCAATGAATCCCAAAG
TGACAGTTACTTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTTCTGATCAATGGAGCTGGCATTTTGGATGCTCATCAGATTGAG
CGAACCATTGCCGTGAACTTCACTGGTTTGGTCAATACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GTAAGGGTGGACCAGGTGGTGTTATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTATCAGGT
CCCTGTCTATTCTGCATCGAAAGCAGCTGTTGTTAGCTTCACTCAATCCATTGCC
>AF264080.1 Drosophila sucinea alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTCGATCGTATTGATAATCCTGATGCCATTGCTGAACTGAAGGCAATCAATCCCAAGG
TGACAGTTACCTTCTTCCCCTACGATGTGACCACATCCTTGGCCGAGACCACCAAATTGCTGATAACCAT
TTTCGCTCAACTGATGACTGTCGTTCTGCTGATCAATGGAGCTGGCATTCTGGACGATCATCAGATTGAA
CGCACCATTGCCGTGAAATTCACCGGCCTGGTCAATACCATCAACGCAATTTTGGACATCTGGGACAAGC
GTAAGGGTGGACCAGGTGGTGTGATCTGCAACATTGGATCGGTGACTGGTTTCAATGCCATGTACCAGGT
CCCCGTCTACTCGGCATCGAAAGCAGCTGTCGTCAGCTTCACTCAGTCCATTGCC
>AF264081.1 Drosophila tropicalis alcohol dehydrogenase (Adh) gene, partial cds
AACCTGGTGATCCTGGATCGTATTGACAATCCTGCTGCCATTGCTGAGCTGAAGGCAATCAATCCCAAAG
TGACAGTTTACTTCTATCCCTACGATGTTACCGCACCCGTTGCAGAGACTACCAAATTGTTGAAGACCAT
TTTCGCTCAATTGAAAACTGTCGATGTTCTGATCAACGGAGCTGGCATTTTGGATGATCATCAGATTGAG
CGTACCATTGCTGTGAACTTCACTGGTTTGGTCAACACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GCAAGGGTGGTCCAGGCGGTGTCATCTGCAACATTGGCTCCGTGACCGGTTTCAATGCGATCTATCAGGT
GGCTGTATATTCCGGCACGAAAGCAGGTGTGGTCAACTTCACTCAATCCATTGCC
>AF264082.1 Drosophila willistoni alcohol dehydrogenase (Adh) gene, partial cds
AACTTGGTGATCCTGGATCGTATTGACAAACCTGCTGCCATTGCTGAACTGAAGGCAATCAATCCCAAAG
TGACAGTTACCTTCTATCCCTATGATGTTACCACACCCTTGACAGAGACTACCAATTTGTTGAAGACCAT
TTTCGCCCAATTGAAGACTGTCGATGTCCTGATCAATGGAGCTGGCATTTTGGATGATCATCAGATCGAG
CGTACCATTGCTGTGAACTTCACTGGTTTGGTCAATACCACCACAGCCATTTTGGACTTCTGGGATAAGC
GTAAGGGTGGACCAGGTGGCGTCATCTGCAACATTGGCTCTGTGACCGGTTTCAATGCCATCTACCAGGT
CCCTGTCTATTCCGCATCCAAAGCAGCTGTTGTTAGCTTCACTCAATCCATTGCC
docker pull pegi3s/fasttree