pegi3s/fasttree

Sponsored OSS

By i3S

Updated 9 months ago

FastTree (http://www.microbesonline.org/fasttree) docker image.

Image
Data Science
Machine Learning & AI

608

This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles)

(Please note that the original software licenses still apply)

Using the FastTree image in Linux

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.

Test data

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 Command

docker pull pegi3s/fasttree