Estimationhyphy_dnds_wrapper.py $input1 $out_file1 "$tree" "$model" $analysis ${GALAXY_DATA_INDEX_DIR}
.. class:: infomark
This tool takes a FASTA alignment file and estimates dN/dS ratio using HYPHY_, a maximum likelihood analyses package.
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.. class:: warningmark
The tool returns an error message if no tree definition or an invalid tree definition is supplied.
Any block/s not containing as many species as mentioned in the tree definition will be omitted from the output.
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For the tree definition, you only need to specify the species build names. For example, you could use the tree *(hg17,panTro1),(mm5,rn3),canFam1)*, if your FASTA file looks like the example below. You may also use **Neighbor Joining Tree Builder** tool to obtain the tree definition::
>hg17.chr7(+):26907301-26907310|hg17_0
GTGGGAGGT
>panTro1.chr6(+):28037319-28037328|panTro1_0
GTGGGAGGT
>mm5.chr6(+):52104022-52104031|mm5_0
GTGGGAGGT
>rn3.chr4(+):80734395-80734404|rn3_0
GTGGGAGGT
>canFam1.chr14(+):42826409-42826418|canFam1_0
GTGGGAGGT
>hg17.chr7(+):26907310-26907326|hg17_1
AGTCAGAGTGTCTGAG
>panTro1.chr6(+):28037328-28037344|panTro1_1
AGTCAGAGTGTCTGAG
>mm5.chr6(+):52104031-52104047|mm5_1
AGTCAGAGTGTCTGAG
>rn3.chr4(+):80734404-80734420|rn3_1
AGTCAGAGTATCTGAG
>canFam1.chr14(+):42826418-42826434|canFam1_1
AGTCAGAGTGTCTGAG
>hg17.chr7(+):26907326-26907338|hg17_2
GTAGAAGACCCC
>panTro1.chr6(+):28037344-28037356|panTro1_2
GTAGAAGACCCC
>mm5.chr6(+):52104047-52104059|mm5_2
GTAGACGATGCC
>rn3.chr4(+):80734420-80734432|rn3_2
GTAGATGATGCG
>canFam1.chr14(+):42826434-42826446|canFam1_2
GTAGAAGACCCC
>hg17.chr7(+):26907338-26907654|hg17_3
GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
>panTro1.chr6(+):28037356-28037672|panTro1_3
GGGGAAGGAACGCAGGGCGAAGAGCTGGACTTCTCTGAGGAT---TCCTCGGCCTTCTCGT-----CGTTTCCTGG----CGGGGTGGCCGGAGAGATGGGCAAGAGACCCTCCTTCTCACGTTTCTTTTGCTTCATTCGGCGGTTCTGGAACCAGATCTTCACTTGGGTCTCGTTGAGCTGCAGGGATGCAGCGATCTCCACCCTGCGGGCGCGCGTCAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGTTCCGTGAGCTGCTTGGTAGTGAAGTTGGTGCGCACCGCGTTGGGTTGACCCAGGTAGCCGTACTCTCCAACTTTCC
>mm5.chr6(+):52104059-52104375|mm5_3
GGAGAAGGGGCACTGGGCGAGGGGCTAGATTTCTCAGATGAT---TCTTCCGTTTTCTCAT-----CGCTGCCAGG----AGGAGTGGCAGGGGAGATGGGCAGGAGCCCCTCCTTCTCACGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGCTGTAGGGACGCGGCAATCTCCACCCTGCGCGCTCGTGTAAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAATTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
>rn3.chr4(+):80734432-80734748|rn3_3
GGAGAAGGGGCGCTGGGCGAGGAGCTGGATTTCTCAGATGAT---TCTTCAGTTTTCTCAT-----CGCTTCCAGG----AGGGGTGGCGGGTGAAATGGGCAAGAGCCCCTCTTTCTCGCGCTTCTTCTGCTTCATGCGGCGATTCTGGAACCAGATCTTCACCTGGGTCTCATTGAGTTGCAGGGACGCGGCTATCTCCACCCTGCGGGCTCTTGTTAGGTACTTGTTGAAGTGGAACTCCTTCTCCAGCTCTGTGAGCTGCTTGGTGGTGAAGTTGGTGCGCACTGCGTTGGGTTGACCCACGTAGCCATACTCTCCAACTTTCC
>canFam1.chr14(+):42826446-42826762|canFam1_3
GGAGACGGAATGCAGGGCGAGGAGCTGGATTTCTCTGAAGAT---TCCTCCGCCTTCTCCT-----CACTTCCTGG----CGGGGTGGCAGGGGAGATGGGCAAAAGGCCCTCTTTCTCTCGTTTCTTCTGCTTCATCCGGCGGTTCTGGAACCAGATCTTCACCTGGGTCTCGTTGAGCTGCAGGGATGCTGCGATCTCCACCCTGCGGGCGCGGGTCAGATACTTATTGAAGTGGAACTCCTTTTCCAGCTCGGTGAGCTGCTTGGTGGTGAAGTTGGTACGCACTGCATTCGGTTGACCCACGTAGCCGTACTCTCCAACTTTCC
.. _HYPHY: http://www.hyphy.org