This notebook illustrates how to use scikit-bio's global aligner to perform progressive multiple sequence alignment. The concept is discussed in more detail in the Multiple Sequence Alignment chapter of An Introduction to Applied Bioinformatics.
First, we'll load up some sequence from the Greengenes 13_5 61% OTUs. These are modified to drop any degenerate characters, which should then show up as gaps in the resulting alignments.
The annotation of this example is very limited as I'm out of time right now. I'll clean it up one of these days.
NOTE: for the sake of runtime, I'm currently computing the alignment from only the first 250 bases of the sequences.
In [1]:
from __future__ import division
from skbio import DNA, parse_fasta, SequenceCollection
sequences = """>229854
GAGTTTGATCCTGGCTCAGATTGAACGCTGGCGGCATGCTTAACACATGCAAGTCGAACGGCAGCATGACTTAGCTTGCTAAGTTGATGGCGAGTGGCGAACGGGTGAGTAACGCGTAGGAATATGCCTTAAAGAGGGGGACAACTTGGGGAAACTCAAGCTAATACCGCATAAACTCTTCGGAGAAAAGCTGGGGACTTTCGAGCCTGGCGCTTTAAGATTAGCCTGCGTCCGATTAGCTAGTTGGTAGGGTAAAGGCCTACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTGAGGGTTGTAAAGCACTTTCAGTGGGGAGGAGGGTTTCCCGGTTAAGAGCTAGGGGCATTGGACGTTACCCACAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCCGCGGTAATACGGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCCGTTAAAAGGTGCCTAAGGTGGTTTGGATAGTTATGTGTTAAATTCCCTGGCGCCTCCACCCTGGGCCAGGTCCATATAAAAACTGTTAAACTCCGAAGTATGGGCACAAGGTAATTGGAAATTCCGGTGGTACCGTGAAAATGCGCTTAGAGATCGGGAAGGGACCACCCCAGTGGGGAAGGCGGCTACCTGGCCTAATAACTGACATTGAGGCACGAAAAGCGTGGGGAGCAACCAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGTCAACTAGCTGTGGTTATATGAATATAATTAGTGGCGAAGCTAACGCGATAAGTTGACCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCTACCCTTGACATACAGTAAATCTTTCAGAGATGAGAGAGTGCCTTCGGGAATACTGATACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGTAACGAGCGCAACCCTTATCTCTAGTTGCCAGCGAGTAATGTCGGGAACTCTAAAGAGACTGCCGGTGACAAACCGGAGGAAGGCGGGGACGACGTCAAGTCATCATGGCCCTTACGGGTAGGGCTACACACGTGCTACAATGGCCGATACAGAGGGGCGCGAAGGAGCGATCTGGAGCAAATCTTATAAAGTCGGTCGTAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGCGAATCAGCATGTCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGGAGTGGGCTGCACCAGAAGTAGATAGTCTAACCGCAAGGGGGACGTTTACCACGGTGTGGTTCATGACTGGGGTGAAGTCGTAACAAGGTAGCCG
>2107103
TTTTCTTGGATTTGATTCTGGTCCAGAGTAAACGCTTGAGATATGTTGATACATGTTAGTTAAACGTGAATATTTGGTTTTTATGCCAACTTTATTTAAGTAGCGTATAGGTGAGTAATATGCAAGAATCCTACCTTTTAGTTTATGTAGCTCGTAAATTTATAAAAGATTTTTTCGCTAAAAGATGGGCTTGCACAAGATTAGGTTTTTGGTTTGCTAAAAACGTTCCAAGCCTAAGATCTTTAGCCGGCTTTCGTGAGTGACCGGCCACATAGGGACTGAGACAATGCCCTAGCTCCTTTTCTGGAGGCATCAGTACAAAGCATTGGACAATGAACGAAAGTTTGATCCAGTAATATCTCGTGAATGATGAAGGGTTTTTGCTCGTAAATTTCTTTTAGTTGAAAGAAAAAAGATATATTTCAACAGAAAAAATCCTGGCAAATCCTCGTGCCAGCAGCCGCGGTAATACGAGAAGGGTTAGCGTTACTCGAAATTATTGGGCGTAAAGTGCGTGAACAGCTGCTTTTTAAGCTATAGGCAGAAAAATCAAGGGTTAATCTTGTTTTTGTCATAGTTCTGATAAGCTTGAGTTTGGAAGAAGATAATAGAACATTTTATGGAGCGATGAAATGCTATGATATAAAAGAGAATACCAAAAGCGAAGGCAGTTATCTAGTACAAAACTGACGCCTATACGCGAAGGCTTAGGTAGCAAAAAGGATTAGGGACCCTTGTAGTCTAAGCTGTCAACGATGAACACTCGTTTTTGGATCACTTTTTTTCAGAAACTAAGCTAACGCGTTAAGTGTTTCGCCTGGGTACTACGGTCGCAAGACTAAAACTTAAAGAAATTGGCGGGAGTAAAAACAAGCAGTGGAGCGTGTGGTTTAATTCGATAGTACACGCAAATCTTACCATTACTTGACTCAAACATTGAAATGCACTATGTTTATGGTGTTGTTTAAGTATTATTTTACTTATAGATGTGCAGGCGCTGCATGGTTGTCGTCAGTTCGTGTCGTGAGATGTTTGGTTAATTCCCTTAACGAACGTAACCCTCAAAGCATATTCAAAACATTTTGTTTTTTTGTTAAACAGTCGGGGAAACCTGAATGTAGAGGGGTAGACGTCTAAATCTTTATGGCCCTTATGTATTTGGGCTACTCATGCGCTACAATGGGTGTATTCTACAAAAAGACGCAAAAACTCTTCAGTTTGAGCAAAACTTGAAAAGCACCCTCTAGTTCGGATTGAACTCTGGAACTCGAGTTCATAAAGTTGGAATTGCTAGTAATCGTGAGTTAGCGTATCGCGGTGAATCGAAAATTTACTTTGTACATACCGCCCGTCAAGTACTGAAAATTTGTATTGCAAGAAATTTTTGGAGAATTTACTTAACTCTTTTTTTTTTTAAGTTGGCTGTATCAGTCTTTTAAAAACTTTGAGTTAGGTTTTAAGCATCCGAGGGTAAAAGCAACATTTTTTATTGGTATTAAGTCGTAACAAGGTAGCCCTACGGG
>696036
AGAGTTTGATCATGGCTCAGGATGAACGTTGGTAGTATGCCTAACACATGCAAGTCGAGCGGAAAGTAGTAGCAATATTACCTTTAGCGGCGAACGGGTGAGTAATACTTATCTTACCTGCCATTTAGTGGGGGATAAAATTCCGCATATTATGAGTAATCATGAAAGGGCTTTCGGGCTCGCTAATTGATGGGGATAAGTCGTATTAGTTAGTTGGTGGGGTAATGGCCTACCAAGACAATGATGCGTAGCCAGTCTGAGAGGATGAATGGCCACAAAGGAACTGAGACACGGTCCTTACTCCTATTGAGGAGGCAGCAGTGGGGAATATTCTGCAATGGGGGAAACCCTGACAGAGCAATACTACGTGAAGGAGGAAGGTCTACGGATTGTAAACTTCTTTACTTAAATGTACTAACCGCAAGGTTTTGCATTTGAGCAAAAAGCGACGACTAACTATGTGCCAGCAGTCGCGGTAAGACATAGGTCGCGAACGTTATCCGGAATTATTGGGCGTAAAGGATGCGTAGATGGTTCAGTAAGTTACTGGTGGGAAATCGAGGCCTAACCTCGTGGAAGTCAGTAATACTGTTGAACTTGAGTGCAGGAGAGGTTAACGGAACTTCATGTGGAGCGGTAAAATGCGTAGATATATGAAAGAACATCAATATAGCGAAGGCAGTTAACTATTCTGCTACTGACATTGAGGCATGAAAGCGTGGGGAGCAAAACGGATTAGATACCCGTGTAGTCCACGCCCTAAACGATGAGTGCTAGATATTGGGAACTTGATTCTCAGTGTCGCTAGGTAACCCGGTAAGCACTCCGCCTGGGGAGTACGCTCGCAAGAGTGAAACTTAAAGGAATTGACGGGGACTCGCACAAGCAGTGGAGCATGTGGTTTAATCCGATACAACGCGTAGAACCTTACCAAGGCTTGACATGTAAGGTAGCAATACTAAATTAGGGAAACCTAGTTGAATTACACAGGTGCTGCATGGCCGTCGTCAGTTCGTGCCGTGAGGTGTATGGTTAAGTCCTATAACGAACGCAACCCTTGTCCTTAGTTGCCAGCATTCAGTTGGGGACTCTAAGGAGACTGCAAGGCATGTTTATGCATGTCTGAACTGAGTAATCAGGAGGAAGGAAAGGATGACGCCTGGTCGTCATGGCCCTTATGCCTTGGGCGACACACGTGCTACAATGGTTAGTACAAAGGGTCGCCAACCCGCGAGGGGGAGCTAATCTCAAAAAACTAACCGCAGTTCAGATTGGAGGCTGCAACTCGCCTCCATGAAGGTGGAATTGCTAGTAATCGTAAATCAGCCATGTTACGGTGAATACGTTCTCGAGTCTTGTACACACCGCCCGTCAAATCACGAAAGTCGGTAATGCCTAAAACCAGTTGATTAACCCGCAAGGGATACAGCTGACAAGGGTAGGATTGGCAATTGGGGTTAAGTCGTAACAAGGTAGCCGTAG
>3190878
TTAATACATGCGAGTTGAACGTGAATTTTTTAATTAAAATGAAAGTAGCGTACTGGTGAGTAACACGTGAGAATCTACCTTTCAAATCAACATAAAATGTTGAATAAAAGCTTCTAAAGCTATAAAGATATGTTTTCGTTGAAAGATGAGCTTGCGCAAGATTAGGTAGTTGGTAAGGTAACGGCTTACCAAGCCAAAGATCTTTAGCTGGTTTGAGAAAATGATCAGCCACATTGGAACTGAAACACAGTCCAAACGTAATATAACGGCAGCAGTAGGGAATTTTGAACACTGAGCGAAAGCTTGATTCAGCCAAGTATCGTGGATGAAGAAGGCTGTCTTTTGGTCGTAAAATCCATTTATATAGTCACATGAAATGTGTCTTTTATTTCGATAAAAGGAAAGATTATGACTTTCTATTGAAAAGTCCCGGCTAATCTCGTGCCAGCAGCCGCGGTAATACGAGAGGGGCAAACGATGTTTAGCATGATTGGGCGTAAAGAGCTTGTAGATGGTTTCTTTTAATTTTATATAAAAGCTCTAAGCTTAACTTTGATTATATATAAAGGAAAGATAACTTGAGTTATGGAAAGGAAAGTAGAATTCTTGGAGGAGAGGTAGAATTTGGTGATATCAAGAGGAATTCCAAAAGCGAAGGCAGCTTTCTTGCCATATACTGACATTGAAGGGCGAAAGCGTGGGTAGCGACAGGGATTAGATACCCCATTAGTCCACGCCGTCAACGATGACCTTTATTTATTGGTTTCTCTTAAAATAAATAAATTATTTTTTAGTTTGATCAGTGAAACAGTTAACGCGTTAAAAGGTCCGCCTGAGGAGTACGATCGCAAGATTAAAACTCAAAAGAATAGACGGGAGCGTTCACAAGTGGTGGAGCATGAAGTTTAATGCGATACAACACGCAAAACCTTACCATTTTTTGATATTTTACTTATCAGTTATTTCTCATGAAATAATGTTTTTTACTAAAGTAAAAATTTGTTTGTATAACAGGCGTTGCATGGCTGTCGTAAGTTCGTACTGTGAAGTGTTGGATTAATTTCCTTAACGAACGTAACCCCTTGGTTTTGTTAAAACTAAAATCTACCGCTAGTCATAAACTAGAGGAAGGGAGGGATCACGTCAAGTCCTCATGACCCTTATAAAATGGGCTACGCTTTTCGTGCTACAATGATAAATACAATAAGAAGCAATAACGAAAGTTGGAGCAAATCTATAAAATTTATCTCAGTTCAGATTGTTCTCTGCAATTCGAGAACATGAAGATGGAATCACTAGTAATCGTAGATCAGCATGCTACGGTGAATATGTAATTACGCTCTGTACTCACAGCCCGTCACACAATGGAAGTAAAATGTATCGGAAATTTGTCAAATATTGTTAGATTTTCTTTTTTAAATTTATTGAATAAATTATTTTAATTAATATCTTTCAACTAAATGGGAACTGATGATATGTTTCATGACTGTTGTGAAGTCGTAACAAGGTAGCGCTAGCGGAAGCTGGTGCTGGAT
>3761685
GATGAACGCTCGCGGCGTGCCTAAGGTATGCAAGTCGAACGCCGACCTTCGGGTCGTGCGTGGCGAACGGGTGAGTAACGCGTGGGAACGTACCGCCGAGATGGGGACAACTCCGCGAAAGCGGAGCTAATACCCAATGGTCCCGGGTCGTACCTCACTGCGTTCGGTACGGATACGATGGACATTCGTATTCCCGCGCCGAGCGTAGCGAGGTGCGACTTGGGTAAAGGAGCAATCCGCTCGGTGAGCGGCCCGCGTCCTATCAGCTTGTTGGTGGGGTAATGGCCTACCAAGGCGATGACGGGTAGGGGGTGTGAGAGCATGATCCCCCACAATGGCACTGAGACAAGGGCCATACACCTACGGGTGGCAGCAATCAGGAATCTTGCGCAATGGGCGAAAGCCTGACGCAGCGACGCCGCGTGGAGGATGAAGGTCGAGAGATTGTAAACTCCTAGCCTTGTGCGTAGCACAAGGGGTTCGTATATCGTTAGTCGGTTACGAAGCCCGTATCGTAAGGCGGTTACGGTTACGTGAAAAACACGTAACCCAATCACGTGACCGAAACGGGCATCGTTACCGTAACCGGCAGACGTTTCACGAATCTCTCGTGTTACGCGCGAGGGGATAAAGTCCCGGCTAACTACGTGCCAGCAGCAGCGGTAAAACGTAGGGGCGAGCGCTATCCGGATTTATTGGGCGTAAAGAGTGCAGGCGCCAGGTTTTTCGTTAAAGCCCCCCGCTCAACGGGGGAACTGCGGAGAATACTGTTTGGCTGGAGGAAGGTAGAGGCTGTCGGAACTCGGGGAGGAGGGGTGAAATCCTATGATCCCCCAAGGAACACCAAAGGCGAAGGCAGACAGCTGGGCCTTTCCTGACGCTGAGGCACGAAAGCTAGGGGAGCGAAACGGATTAGATACCCGTGTAGTCCTAGCCGTAAACGATCCCCGCTAGATTTTGGCATCTGTCAGAGTCGAAGCTAACGCATTAAGCGGGGCGCCTGGGAAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGACGGGGACCCGCACAAGCGGTGGAGCGCCTGGTTTAATTCGATGATAACCGAAGAACCTTACCAGGGCTTGACATCCCGACAGAAATCCCGACGAAAGTTGGGCCCCCCGCAAGGGCTGTCGGGACAGGTGTTGCATGGCTGTCGTCAGCTCGTGCCGTGAGGTGTATGCTTAAGTGCCGAAACGAGCGCAACCCCTACCCCATGTTAGAAATGTCGTGGGGGACTGCCTCCGTAAGGGGGAGGAAGGTGGGGACGACGTCAAGTCAGTATGGCCCTTATGCCCTGGGCAACACAGACGCTACAATGGCGGCTACAACGGGTTGCAATGTCGTAAGGCGGAGCTAATCCTAAAAAGCCGTCTCAGTTCGGATTGGGGGCTGAAACCCGCCCCCATGAAGTTGGAATCGCTAGTAATGGCCGGTCAGCTATACGGCCGTGAATACGTTCTCGGGTCTTGTACACACCGCCCGTCA
>3779572
GGAACAACAACTGGAAACGGTTGCTAATACCCCATAGGCTGAGGAGTCAAAGGAGGAATCTGCCCTAGGAGGGGCTTGCGTCTGATTAGCTTGTTGGTGAGGCAATGGCTTACCAAGGCAAGGATCAGTAGCTGGTCCGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGTTGAGGCCTACGGGTCCCGAACTTCTTTTCTCGGAGAAGAAGCAATGACGGTATCTGAGGAATAAGCATCGGCTAACTCTGTGCCAGTAGCCGCGGTAAGACAGAGGGTGCAAGCGTTATCCGGTAAAGCGTCTGTTAGGTGGCTTTTCAAGTCCTCCGTCAAATCCCAGGGCTCAACCCTGGACAGGCGGTGGAAACTACCAAGCTGGAGTACGGTAGGGGTAGAGGGAACTTCCGGTGAAGCAGTGAAATGCGTTGAGATCGGAAAGAACACCACTGGCGAAAGCACTCTGCTGGACCGACACTGACACTAAAGGACGAAAGCTAGGGGAGCGAATGGGATTAGAGACCCCGATAGTCCTAGCCGTAAACGATGGATACTAGGTGTTGTGCGTATCGACCCGTGCAGTGCTGTAGCTAACGCGTTAAGTATCCCGCCTGGGAAGTATGTTCGCAAGAATGAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAAAGCGGAGAACCTTACCAGGGCTTGACATGTTTTGCGAATCTCTCTTGAAAGAGGGGAGTGCCTTCGGGAACGCGGACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGCCGTAAGGTGTTGAGTTAAGTCTCGCAACGAGCGCAACCCTCGTGTTTAGTTGCCACCATGGATTTTGGAACCCTGAACAGACTGCTGGTGTGAAGCCGGAGGAAGGAGAGGATGACGTCAAGTCCTCATGCCCCTTATGCCCTGGGCGACACGCGTGCTACAATGGGCGGGACAAAGGATCACGATCCCGCGAGGGTGAGCTAACTTGTTCTCAGTTCGGATTGCAGGCTGCAACTCGCCTGCATGAAGCAGGAATCGCTAGTAATCGCCGGTCAGCCATACGGCGGTGAATTCGTTCTCGGGCCTTGTACACACCGCCCGTCACACTAGGGAAGCTGACCATGTCTGAAGTTCTTACCTGAACCGCAAGGAGGGGTATGCCCAAGGCGAGGCTAGTAACCGGAGTGAAGTCGTAACAAGGTAGCCGTACTGGAAGGTGCGGCTGGATTACCTCC
>4251079
AGTGGCGAACGGGTGCGTAACGCGTGGGAATCTGCCGAACAGTTCGGGCCAAATCCTGAATCAAGCTAAAAAGCGCTGTTTGATGAGCCTGCGTAGTATTAGGTAGTTGGTCAGGTAAAGGCTGACCAAGCCAATGATGCTTAGCTGGTCTTTTCGGATGATCAGCCACACTGGGACTGAGACACGGCCCGGACTCCCACGGGGGGCAGCAGTGGGGAATCTTGGACAATGGGCGAAAGCCCGATCCAGCAATATCGCGTGAGTGAAGAAGGGCAATGCCGCTTGTAAAGCTCTTTCGTCGAGTGCGCGATCATGACAGGACTCGAGGAAGAAGCCCCGGCTAACTCCGTGCCAGCAGCCGCGGTAAGACGGGGGGGGCAAGTGTTCTTCGGAATGACTGGGCGTAAAGGGCACGTAGGCGGTGAATCGGGTTGAAAGTTCAAGTCGCCAAAAACTGGCTCCATGCTCTCGAAACCAATTCACTTGAGTGAGACAGAGGAGAGTGGAATTTCGTGTGGAGGGGTGAAATCCGGAGATCTACGAAGGAACGCCAAAAGCGAAGGCAGCTCTCTGGGTCCCTACCGACGCTGGGGTGCGAAAGCATGGGGAGCGAACAGGATTAGATACCCTGGTAGTCCATGCCGTAAACGATGAGTGTTCGCCCTTGGTCTACGCGGATCAGGGGCCCAGCTAACGCGTGAAACACTCCGCCTGGGGAGTACGGTCGCAAGACCGAAACTCAAAGGAATTGACGGGGGCCTGCACAAGCGGTGGAGCATGTGGTTTAATTCGATACAACGCGCAAAACCTTACCAGCCCTTGACATATGAACAAAAAAACCTGTCCTTAACGGGATGGTACTGACTTTCATACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTTGGTCAAGTCCTATAACGAGCGAAACCCTCGTTTTGTGTTGCTGAGACATGCGCCTAAGGAAAAAGTCTTTGCAACCGAAGTGAGCCGAGGAGCCGAGTGACGTGCCAGCGCTACTAATTGAGTGCCAGCACGTAGCTGTGCTGTCAGTAAGAAGGGAGCCGGCGCCTTTCGAAGCACTTTCTAGTGTGAACCGAACGTCCCGCGTTCCGGCTTGTTCGAATCGCGTCACGAGTCTACAAGCCCCACTGATACCTACCTATAGTGACGTCAAAGTACCAGTGACGGTGACTTGGTTGCGTAACGTAATATGGATTCAGTCAGCGAAACTCCCTCCAACTCAATCAATATCAACAACATGTCGTGACGAGCCTGACTACACTCCACCTGACGGTACTACACTATCTATCAGTAGAGCGCCTTGCGCGATACGGCTTTTTGGCCGTATCTTGCAGGTGACGACGACGTCGAGTTGGCGGCGGAGGAAGACTCGGCATTCAGGCGAGCCGCCCGGTGGTGTGGTACGTAGTGGTAATAGTACGCCCCGCCCGTCACACCCTTCAAGCTCCGAAACAAACAAAAAGGTGCGTGCCGCACTCACGAGGGACTTGCCAGTGATATACTGAAGGAAGGTGGGGATGACGTCAAGTCCGCATGGCCCTTATGGGCTGGGCCACACACGTGCTACAATGGCAATTACAATGGGAAGCAAGGCTGTAAGGCGGAGCGAATCCGGAAAGATTGCCTCAGTTCGGATTGTTCTCTGCAACTCGGGAACATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCATGCCGCGGTGAATATGTACCCGGGCCCTGTACACACCGCCCGTCACACCCTGGGAATTGGTTTCGCCCGAAGCATCGGACCAATGATCACCCATTCCTTGTGTGTACCACTAGTGCCACAAAGGCTTTTGGTGGTCTTATTGGCGCATACCACGGTGGGGTCTTCGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGTG
>4336814
ACGCTGGCGGCACGCCTAATACATGCAAGTCGAACGAAGTAGCAATACTTAGCGGCAGACGGGTGAGTAACATGTGGGTATCTTCCCTTTGGTGAGGAATAACACGAGGAAACTTGTGCTAATACCTCATAAGTCTTTACAGAGAAAGCTTTATGCGCCGATGGATGAGCCCGCACTTGATTAGTTTGTTGGTGGGGTAATAGCCTACCAAGACTATGATCAATAGCTGATTTGAGAGGATGATCAGCCACATTGGGACTGAGACACGGCCCAAACTCCTACGGGAGGCAGCAGTAGGGAATCTTGCACAATGGAGGAAACTCTGATGCAGCGATGCCGCGTGAGTGAAGAAGGCCCTTGGGTTGTAAAGCTCTTTCGTCGGGGAAGAAAATGACTGTACCCGAATAAGAAGGTCCGGCTAACTTCGTGCCAGCAGCCGCGGTAATACGAAGGGACCTAGCGTAGTTCGGAATTACTGGGCTTAAAGAGTTCGTAGGTGGTTAAAAAAGTTGGTGGTGAAAGCCCAGAGCTTAACTCTGGAACGGCCATCAAAACTTTTTAGCTAGAGTATGATAGAGGAAAGCAGAATTTCTAGTGTAGAGGTGAAATTCGTAGATATTAGAAAGAATACCGATTGCGAAGGCAGCTTTCTGGATCATTACTGACACTGAGGAACGAAAGCATGGGTAGCGAAGAGGATTAGATACCCTCGTAGTCCATGCCGTAAACGATGTGTGTTAGATGTTGGAAATTTATTTTCAGTATCGCAGCGAAAGCAATAAACACACCGCCTGGGGAGTACGACCGCAAGGTTAAAACTCAAATGAATTGACGGGGACCCGCACAAGTAGTGGAGCATGTGGTTTAATTCGAAGATACGCGCAGAACCTTACCAACACTTGACATGTTCGTCGCGACTCTAAGAGATTAGAGTTTTCGGTTCGGCCGGACGAAACACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTCACTTTTAGTTGCTACCATTTAGTTGGGCACTCTGAAAGAACTGCCAGTGATAAGCTGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCCTTACGTGTTGGGCTACACACGTGCTACAATGGGTACACACCGCCCGTCACACCATGGGAGTTGGTTCTACCTTAAGGCAAAGTTTAAAACCTTTGACCACGGTATAGTCAGCGACTGGGGTGAAGTCGTAACAAGGTAGCCGTAGGGGAACCTGCGGCTGGATTACCTCCTTTCT
>4363260
CCTTGGGGAGAATAACAACTGGAAACGGTTGCTAAAACTCCATAAGCTGAGAAGTTAAAGGTTAACACCACCTAAGGATGGGCTTGCGTCTGATTAGCTAGTTGGTAAGGTAATGGCTTACCAAGGCAACGATCAGTAACTGGTCTGAGAGGATGATCAGTCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGAGGAATTTTCCGCAATGGGCGAAAGCCTGACGGAGCAATGCCGCGTGGAGGATGACGGCCCGTGGGTTGTAAACTCCTTTTCTTAGAGAAGAAATTTGACGGTATCTAAGGAATAAGCATCGGCTAAATTATTGGCCCCTACATTAGTGATTTTGTAGGTAAACTTGGCTCATAACGGTGAAACCCTAACGCGTCTGCGGTTTATTCTGAATTTTCTAAATTCCGAATTTCCTTTTTCTTTTGAAAAAGGGATGGCGAGGGCAATACCGTGGGAAGTCTATTCAGTGAAAACGTTAGTCAATTCATTAATTTTAACAGACCCGCTAGCGTTATGTTTGGTATTTAGATGACGGTACGAAACGAAGGTACTGAATCTTGTCGAATCGCAACTCAATCTTTTTCTAAAGAGGAACACGAATTGTTACAAAATTGTTTCAAACAAAATTTTAATATATCGGTCCAAATTGAAGATTGGGGAAGAACAAAAGACGGTTCAATTTCTTACTCACTTGCCATTTTAAGTCGAGGAGGAAATTTTAAGAAATTTCGTGATGTTATTTACGATATCGTAAATGCCGAAGTACCAAGCATGCTTTATAAGCTGTAATGACCCCGTAACGACTGAGAAAATGTTTTTTTCGAAAAACAAAGTACGAGATATTTTCTTTGAATAAATAAGAAAGTATAATACGCCGAGCGCTTGATTTCATCATCAAGATGATGGTATAGTCTATGCTCTAGGAAACTAGGGATTATCATGAACTCCGTGCCAGCAGCCGCGGTAAGACGGAGGATGCAAGCGTTATCCGGAATGATTGGGCGTAAAGCGTCTGTAGGTGGTTTTTAAAGTCGAATGTCAAAGATCAGGGCTTAACCCTGATTCGGCATTCGAAACTCAAAAGCTTGAGTTCGGTAGAGGCAGAGGGAATTCCCGGTGTAGCGGTGAAATGCGTAGATATCGGGAAGAACACCAACGGCGAAAGCACTCTGCTGGGCCGAAACTGACACTCAGAGACGAAAGCTAGGGGAGTGAATAGGATTAGATACCCTAGTAATCCTAGCCGTAAACGATGGATACTAAGCATTGGGCGCTAAAACGTTCGGTGCTGTAGCTAACGCGTTAAGTATCCCGCCTGGGGAGTATGCTCGCAAGAGTGAAACTCAAAGGAATTGACGGGGGCCCGCACAAACGGTGGAGCATGTGGTTTAATTCGATGCAACGCGAAGAACCTTACCAGGGCTTGACATGCTACGCATTCTTTGGAAACAGAGAAGTTCAAACGTAGACACAGGTGGTGCATGGCTGTCGTCAGCTCGTGCCGCGAGGTGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTATTGTTAGTTGCCATTGGGAAACTAGCAACACTGCCGGTGATAAGCCGGAGGAAGGTGAGGACGACGTCAAGTCATCATGCCCCTTACGCCCTGGGCTACACACGTGCTACAATGGCCAGGACAAAGAGACGCAACCCCGCAAGGGTAAGCTAACCTCAAAAACCTGGTCTCAGTTCGGATTGTAGGCTGCAACTCGCCTACATGAAGCCGGAATCGTTAGTAATCGCCGGTCAGCCATACGGTGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCATGGAAGCTGACTGGGCCCGAAGTCGTGGATTCACGCCTAAGGCATAGTTAGTGACTGGGGTGAAGTCGTAACAAGGTAGGGCTACTAAGGTGGCCCTGGATCACCTCCTT
>4363563
AGAGTTTGATCATGGCTCCGAGTGAATGCTAGCGGAAGGCTTGACACATGCAAATCGAACGGCGTGAAAACGCGCAGTGGTGTCTTGGTGAGTAATATATGGGGATCGAAGCCTGGTTTCTGGGATTTAAAATACCGATTAAAAGATTTAAATTGCCCAGGCTAGACCTCGTTTTATAATTAGGTAGTTGGTAGTGTAATAGACTGCCAAGCCATCGATGTTTAGCTGGTTTGGGAGAACGATCAGCCACAATGGGACTGAAATACCGCCCGTCTTCTTCGAGGGGGCAGCAGTGGGGAATCCTGGACAATGAGCGAAAGCTTGATCCGGCAATTCTGCATGTATGATGAAGGCCCTGACACGTCGTAAAGTACTAACATCGAGGATAATAATGACGGTACTCGATTAAGAAGTCCTGACTAACTTCGTGCCAGCAGTCGCGGTAAAACGGAGAGGACAAGTGTTATTCGTATTGACTGGGTGTAAGGGTACGTAGGTGGTTGTTTAAGTTAGAAATGAACAAACGAATTTCTAAAACTATCCGACTAGAGTTATGGGGAGGAAAGCGGTACTTCCAGTTTAGAAGTGATATTCGTTTGAGATTGGGGGGACCAACACTAGGCGACGGCTGCTTTTCATTCATAGACTGACACTGAGGTACGAAAGCGTGGGGAGCGGACGGGATTAGATACCCTGGTAGTCCACGCCCTGACCGATGAATATTAATCGTTCGCTTTTTAGCGGGTGATTGAGCTAACGCGTAAATATTCCACCTGAGGACTACGGCCGCAAGGTTAAAACTCAAAGAAATTGGCGGAAGATTGTTTAAGCGGTGGAGTATGTGGTTTAATTTGATAATACGCAGAGAACCTTACCAATCCTTGAGGATACGTAAATACGAGTGTAATTACTTTTTTCGGCTTAGACTCTTAACGGGAGATAAGCTAGACGTATTCCAGGCGTTGCATGGCTGTCGTAAGTTCGTGTCTTGGGATGTGTGGTTAACTCCATGAACGGACGCAACCCTTGTCCCTAATTACTTTAGGGAGCTGATTTGAGAGACCTTGTGGAAGCAGAGGAGTATGTCAAGTCATTATGACCCTGATGGATTGGGCTACACACGTACTACAAGGGTAATTACAAAGAGAAACAAGACCGCGAGGTGGAGTGAATCTCGAAATGTTACCATAGTTCGGATTGTTTTTTGCAATAAAAACATGAAGGCGGAATCGCTAGTAATCGCGGAATAGAATGTCGCGGTGAATAATAAGACCGATCTTAGTACACACCGCCCGTCACGCCATGGGAGTTGGCGTAGTTTGAAGAGCTAAGCATGTGTTTTCAAAGGGCCCGGTTTCGTTTGATTGAATTAAAATATCGGCCTCGTGGCATGTGAACTGGTGTCGACAATTACGTTGGTAACTGGGGTGAAGTCGTAACAAGGTA
>4391683
AGAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCATGCCTAACACATGCAAGTCGAACGAGACCTTCGGGTCTAGTGGCGCACGGGTGCGTAACGCGTGGGAATCTGCCCTTGGGTTCGGAATAACAGTTAGAAATGACTGCTAATACCGGATGATGACTTCGGTCCAAAGATTTATCGCCCAAGGATGAGCCCGCGTCGGATTAGCTAGTTGGTGAGGTAAAAGCTCACCAAGGCGACGATCCGTAGCTGGTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCTTACGGGAGGCAGCAGTGGGGAATTTGGACAATGGGCGAAAACCCTGATCCAGCAATGGCCGCGTGGAGTGATGAAGGGCTTAGGGTTGTAAAGGCTCCTTTTAACCCGGGGATGATAATGAACAGTACCCGGGAGAAATAAAGCCCCCGGGGTTAACTTCCGTGGCCAGCAGCCCGCCGGTAATACGGGAGGGGGGCTAGCGGTTGTTTCGGAAATTACTGGGGCGTAAAAGCGCCACGTAGGGCGGCTTTTGGTAATTTAAAAGGTGAAAAGCCCCGGGGGCTTCAACTTCCCGGAAATTTGGCCCTTTAAAAATTGCATCCGCTAGAAATTGTGGGGAGAAGGGAAGTTGGAAATTCCCCAGTGGAAGAGGGTGAAAATTTCTCTAAATAATTTCTCGAAGAAAACCCCCGTGGGCGAAAGGCGAACTTTTATGGGGCCACATATTTGGACGCCCTGAAGAGTGGGCGAAAAGCGTGGGGGGGGGCAAAACACGGAATATATAATAAACCCCTGGGTAGGTCCCACCGCCCCTGTACCGATGATGACTAGTCTTGTCGGGCCGTATTAGCTTTTCCCGGGTGGCCGCAGCTTACGGGCGTTATAAGTCCATCCCCCCGTGGGGGAGTACCGCCCCGCAAGGTTAAAAAACTCCAAGAGAAATTGGCGGGGGGGCCTGCCACAAGGCGGGTGGGAGCATGTGGGTTTTATTTCGAAAGCAACCGGCGCCAGGACCTTTTACCCAGCTTTTTGCACATGGTTAGGACGTGTTTTCCCAGAGAGATGGATTCCTTCCCTTACGGGGACTAAACACACCAGGTTGCGCCAATGGCTGTTCGTTCCAGCCTCGGTGTCGGTGAAGATGTTTGGGTTAAGTTCCCGCAACCGAAGCCGCAACCCCTCGTTCTTTTAGTTGCCCAATCATTTAGTTGGGCACTCTAAAAGAAAACTTGCCGGTGATAAGCCGGAGGAAGGGGGGGGATGACGTCAAGTCCTCATGGCCCTTACGCGCTGGGCTACACACGTGCTACAATGGCGGTGACAGAGGGCAGCAAACCCGCGAGGGTGAGCTAATCTCCAAAAGCCGTCTCAGTTCGGATTGTTCTCTGCAACTCGAGAGCATGAAGGCGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCAGGCCTTGTACACACCGCCCGTCACACCATGGGAGTTGGTTTCACCCGAAGGCGCTACGCTAACCGCAAGGAGGCAGGCGACCACGGTGGGATCAGCGACTGGGGTGAAGTCGTAACAAGGTAACC
>4423155
AGAGTTTGATCTTGGCTCAGGATGAACGCTGGCGGTATGCCTGAGATATGCAAGTCGAGCGCAGTCCCGACCGCAAGGTCGTGGATTCAGCGGCGGACGGCTGAGTAATACATAGAAATCTGCCCCTTTCTGGAGGATAGCCCCGCGAAAGCGGGGGTAATACTTCATAGTGTCATGCCTAGCATGACTAAAGGACGTAACTGTTCGGAAAGGGATGAGTCTGTGTCCTATCAGGTAGTTGGTAGGGTAATGGCCTACCAAGCCAATCACGGGTAGCTGGTCTGAGAGGATGGCCAGCCAGAGGGGGACTGAGACACGGCCCCCACTCCTACGGGAGGCAGCAATCAGGAATAGTCGGCAATGGACGAAAGTCTGACCGCGCGATACCGCGTGTAGGATGAAGCTCTCACGAGTGTAAACTACTGTGGAGAAGGAAGAAGTCTGGCGTAAGCCAGATTGACGGTACTTCTCTAGAAAGGGGCCGCTAACTGCGTGCCAGAAGCGTCGGTAATACGTGGGCCTCAAGCGTTATCCGGTATCACTGGGCATAAAGGGTCGTGTAGGTGTCTTGTTAAGTTTCTGTTTAAAGATCAAGGCTCAACCTTGGGAAAGGCGGAAAAACTGGCAAGATAGAATTTCCTTAAGGGGGATCGGAACTGAGAGAGGAGTAGTGAAATGCGTTGATACTCTCGGGAACACCAGTGGCGAAGGCGGATCTCTGGAAGGAAATTGGCACTGAGACACGAAAGCTAGGGGAGCGAAGCAGATTAGAGACCTGCGTAGTCCTAGCCCTAAACGAATGCTTGCTAGCTGCATGATCTCAGAACTTAGACGATAGGCAATAGACGACAGACGATAGTCATAATATGACTATTGTCTATAGTCTAACGTCTGTAGTCTGCGTTCTGATATCGTGTGGCGAAGGAAATCCGTTAAGCAAGCCGCCTGGGGAGTACGGCCGCAAGGCTAAAACTCAAAGGAATTGGCGGGGAGGCACACAACCAGTGGAACATGTGGTTCAATTCGATACAAACCGAAGCACCTCACCAGGGTTTGAAATGCTAGAGTTCTATACCGATGAAAGTTGGTAGATGCGCAAGCAGGCTAGCACAGGTGCTGCATGGCTGTCGTCAGCTCGTTCCGTGAGGAGTGCCCTTAAGTGGGACAACGAGCGCAACCCCCGTCTCATGTTATATTTGTCATGAGATACTGCCCGAGCTTTGCTCGGGAGGAAGGAGGGGCAGACGTCAAGTCAGCATGGTCCTTATACCCTGGGCTACACACATGTTACAATGAAAGGAGCGACGGGCTTTGCAAACCGGTAACGGCCAGCGAATCCCTTAAACCCTTTCTCAGTGGGGATTGAGGTCTGAAACTCGACCTCATGAACGTGGAATTGGTAGTAATCGCGGGTCAGCTACACCGCGGTGAATACGTTCTTGCCTCTTGTACACACCGCCCGTC
>4452949
AAACAAACAAGAGTTTGATCCTGGCTCCGAATGAACGCTAGCGATAGGCCTAACACATGCAAGTCGAACGCATACTTTAGAGTATGAGTGGCAGACGGGTGAGTAACGCGTGAGACATCTACCTTACAGCCCGGTATAAATATCTATATAGAGGCGAAAATCTTTATATATGAGTGAATCCCGGATATTTTGAATAAAAAAAAAGGCAAAGAACCGTTGTAAGATGAGCTCGCGTAGGATTAGGTAGTTGGTAAGGTAAAAGCTTATCCAAGCCGATGATCCTTAGCTAGTTCTGAGAGGATGATCAGCCACACTGGGACTGAGACACGGCCCAGACGCTTTCGAGCGGCAGCAGTGAGGAATTTTGGACAATGGGCGAAAGCCTGATCCAGCTATATCGCATGAATGAAGAAGGCTCAATTGGTTGTAAAATTCATAGTTTCATTGTAGATTATGACATTGATGAAATGAATAGTCCCGGCCAACTCCGTGCCAGCAGCCGCGGTAATACGGGGGGGGCGAGCGTTATTCGAAATGATTGGGCGTAAAGAGCACGTAGACGGTTTTTTAAGTGGACATTATATCTTTTTTGTTCTCTAAGGATAAAAAAGAAAGGATTATGGAAATATTTCTGTACTCGGGAAAAAGACCAAGGCTCAACCATGGTGTTTCCCGCCAAACTAAAAAACTAGAGTAAGTTAGAGGAAAGTGGAATTCCTGGAGGAAAGGTTAAATTTTATGATATCAGGAGGAACGCCCAAAGCGTAGGCAACTTTCTACTGCTTAACTGACGTTGAGGTGCGAAAGCATGGGGATCAAAGGGGATTAGATACCCCTGTAGTCCATGCCGTCAACTATGAGAATTCACTCTTAGAACACTGTGTATTCCTTTGAACGATGGGTTTTTTCTCATCAATCAAAGGAATACGCAGTTCGTTTTAGGGGTTCTAGCTAACGCGTTAAATTCTCCGCCTGAGGAGTACGACCGCAAGGTTAAAACTCAAAGGAATAGACGGGGGCTCACACAAGTGGTGGAACATGTGGTTTAATTCGACACAACGCGCAAAACCTTACCAGCCCTTGACATAAGCTTGAATACATCTTTTATCGGATAATTATACAGTTTACAGGCGTTGCATGGCTGTCGTCAGCTCGTGTCGTGAAACCAATATATAAAAAAATAATCGCGACCTAGAGGAGTGATCCTCTAGTAAAATCCAACTCATAACGGTGGAACCCTTGTGTAAAGGCATTGATTTACAGATATATCAAAATAAGCAAGGGCAATACCGTGGGAAGTCGATAGATAATGTATTCTTTTGTTTTACGTAGTAAAACAACAAAAATAATAAAAGAAAGATCTATCCTTTTTTGTATTAAAAAAATACAAAAATCCACCAAAAAAAAGGTATTATAAACGAACATTTTTTTGTGTGCTATCTTCATATATTATATTCTTATAGACTTTATATATATATAACTTTCTTTCATTATCTAAACATAATACTGTAATATTTGACCCCGTAACGACTTTGTTATTTTTTTTACAAAAAAAGGCAAGATATCGGATCTTATTGAATATAAAAATTGAATATGCCGGTATAACACGTTGGCTCTTGTAACACTATTTTGAAAAAGATAGTAACAAGATGAAGGTATAGTCTATTCCTTATAGTAATATAGGGGTTATTGCAGTAATCATAAATGGATCCTTTTTCTAACCTGTTCCTTCCCTTTTCATCGCTTAAAAAAAAAAGGACTATTTTTTGACAGGGAAGGGATACCAGATTAGGATACCAGGTTGGAGATTTTGTAAAAGAATACAAAATTGTATTTTCTATAATACAAAATGATCCTTTTTGTTTTGTTTTACGTAGTAAAACAACAACCTTCTATTCGCTTTTTTTTTTTTTAAAAAAAGGGCAGAGATACCTGGTTACTGTAAACATTGGAGATGTTTGGTTAAGTCCTTTAACGAGCGCAACCCTTTTGAAATGTTGGTAGTAAAGAACAACTCTTTAACCACTCTTTTCATACTGCCGGTTATATACTGGAGGAAGGGAAGGATAACGTCAAGTCGTCATGACCCTTATGGGCTGGGCTACACACGTGTTACAATGGTAATTACAAAGGGAAGCAATGGTGCGAATCGGAGCGAATCCTTAAAAATTACCTCAGTTCAGATTGTTCTCTGCAATTCGAGAACATGAAGATGGAATCACTAGTAATCGTGGATCAGCACGCCACGGTGAATCTGTACCTGAGCCTTGTACTCACCGCCCGTCACACTCTGGAAGTCG
>4459468
GAGTTTGATCCTGGCTCAGAACGAACGCTGGCGGCGTGTCTTAACACATGCAAGTCGAACGCGAACGGGTTCTTCGGGACCTTAGTAGAGTGGCGCACGGGTGAGTAACGCGTAAGCCCCTCTACCTCGGCATCTGGAATAACTCACCGAAAGGTGAGCTAATACCGGATACGTTGGCAACAAGAAAGGTGGCCTCTGAATATGCTACCGTGCCGGGATGAGCTTGCGTACCATTAGCTAGTAGGTAGGGTAATGGCCTACCAAGGCGACGATGGTTAGCGGGTCTGAGAGGATGATCCGCCACACTGGAACTGGAACACGGACCAGACTCCTACGGGAGGCAGCAGTGAGGAATATTGCGCAATGGGGGCAACCCTGACGCAGCGACGCCGCGTGGATGATGAAGGCCTTCGGGTCGTAAAATCCTGTCAGTGGAAAGAAGTGCCACGATGGCTAATATCCATTTTGTTTGACGGTACCGCCGAAGGAGCACCGGCTAACTCCGTGGCCAGCAGCCGCGGTAATACGGAGGGGGCAAGCGTTGTCGGAATAACTGGGCCTAAAGCCGCGCCGTAGGCGGGTTTGTTAAGTCAGATGTGAAAGCCCTCGGCTCAACCGGGGACGTGGCATTTGAACTGGCCAACTTGAGTACTGGAGGGGGGGGGAATCCCGTGTGAGGTTGCGAAAGGCGTGGGGAGGCAAACAGGATAGATTACCCTTGGATAGTTCACGCGTAAACCGATGAAGAGCTAGGTGTTGGGACGTTTATTCGTCTTCATTGCCGCAGCTAACGCATTAAAGTTCTCCGCCTGGGGAGTTACGGTCGCAAGATTAAAACTCAAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGTATGTGGTTTAATTCGACGCAACGCGAAGAACCTTACCTGGTCTTGACATCCCGGGAATCTGCTGGAAACAGTGGAGTGCCTCGCAAGAGGAGCCTGGTGACAGGTGCTGCATGGCTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCTTGTCTTTAGTTGCCAGCATTAAGTTGGGCACTCTGAAGAGACTGCCGGTGTCAAACCGGAGGAAGGTGGGGATGACGTCAAGTCCTCATGGCCTTTATGACCAGGGCTACACACGTACTACAATGGCATATACAGAGGGCAGCGACATCGCGAGGTGAAGCCAATCCCTAAACTATGTCTCAGTCCGGATTGGAGTCTGCAACTCGACTCCATGAAGTTGGAATCGCTAGTAATCGCGGATCAGCACGCCGCGGTGAATACGTTCCCGGGCCTTGTACACACCGCCCGTCACACCACGGGAGTTGGTTGTACCAGAAGCAGTTGAGCCAACCGCAAGGAGGCAGGCTGCCAAGGTATGGCGAGTAACTGGGGTGAAGTCGTAACAAGGTAGCCCTAGGGGAACCTGCGGCTGGATCACCTCCTT
>426860
CATGCAAGTCATAGGCTCGCAAGAGTACTGGCACAAGGCTCAGTAACACGTCGATAATCTGCCTTACGGTCTGGGATATCCTCGGGAAACTGAGGTTAAACCCGGATAAGAGCTACGCACTGGAAGGTCGTTGCTCGTAAAAGTAATGCCGTAAGATGAGTCGGTGGCTGATTAGGCTGTTGGCGAGGTAACGGCTCACCAAACCTAAGATCAGTAGGGGGGATGGAAGTCCTAGCCCCGAGAAGGGCACTGAGATAAGGGCCCTAGCCCTAAGGGGTGCAGCAGCCGGGAAACCTTTGCAATGCACGAAAGTGTGACAAGGGAACTCCACGTGCATATCGTCACTTGATGGTATGCTTTTGTTAAGTGTAAGGAGCTTAGCGAATAAGTGGTGGGCAATACCGGTGCCAGCCGCCGCGGTAATCCCGGAGCCACGAGTGGGGACCAGTTCTATTGGGTCTAAAGCGTCCGTAGTCGGTCGTGAAAGTTTCTTGTGAAATAGTTCTTCTTAAGGGAACTGAGTGCAAGGAATACTCCACGACTTGAGACCGGGAGGGGGCAGGAGTATGCCAAGGGGAGCGGTAAAATGCGATAATCCTTGGTAGACTACCAATAGCGAAGCACCTGTCCAGAACGGGTCTGACGATCAGGGACGAAAGCTAGGGGAGCAAAAGGGATTAGATACCCCTGTAGTCCAGCCGTAAACACTGCAAACTAAGTGTTACATATCCTTCGTGGGTATGTAGTGCTGGAGCGAAGGCGTTAAGTTTGCCACCTGGGGAGTACGGCCGCAAGACTGAAACTTTAAGGAATAGGCGGGGGCGCACTACAAGGAGTGACGCGTGCGGTTTAATTTAACTCTACACAGAAAACCTCACCAGGAGCGACGGCAGTATGAAGGTCAGATTAAAGGTCTTACCTAACGAGCCGAGAGATGTTGCATGGCCGCCGCCAGTTCGTGCCGCAAGGTGTCTGGTTAAGTCCAGTAACGAACAAGACCTGCGTCCATATTTGCTAGCGAGTCGTTTCGATGATCGAGCACTATATGGGGACTGCCTGGGTAACCAGGAGGAAGGTGCAGGCAACGGTAGGTCTGTGTGGCTCGAATCCTCTGGGCTACACGCGCGCGGCAATGGCAACGACAATGGGATGCAACTCCGTAAGGAGAAGCCAATCCTCGAAACGTTGCCCTAGTTTAGATTGAGGGCTGTAACTCGCCCTCATGACACCGGAATTCCTAGTAATCGCTCGTCAACAGCGAGCGGTGAATACGTCCCTGTGCCTTGCACTCACTGCCCGTCAAGCCAATCGAGCAGGGTCCGAGTGAGGCTCAATCTTCGGGTTGATACGAACTCGGGCTCAG
>1928988
TTCCGGTTGATCCTGCCGGACCCGACTGCTACTTGGGTGAGAATAAGCCATGCAAGTCGAATGGAATACCAAAATATTCCATAGCAAACTGCTCAATAACACGTGATCAACTTACCCTATGGAAAACAATAACCTCTGGAAACGGAGGATAATGGTTTATAGTTGAAAAGGCTTGGAAAAGTTTTTCAATAAAAGGGAATAATAAAAATGGTTATTATTTTGCCATAGGATAGGATTGCGGTCGATCATGGCTGTTGGTGAGGTAATGGCTCACCAAACCAATAATCGATAGGGGCCGTGAGAGCGGGAGCCCCGAGATGGGTACTGAGACAGCGACCCAGGCCTTACGAGGTGCAGCAGGCGCGAAAACTCCGCAATACGCGAAAGTGTGACGGGGTTACCCAAGGTGCTTAATTTTTAAGCTGTGGTAAGTGTGTAATGTACCTTACTAGAAAGGAGAGGGCAAGGCTGGTGCCAGCCGCCGCGGTAAAACCAGCTCTTCAAGTGGTCGGGATAATTATTGGGCTTAAAGTGTCCGTAGCTTGTATAATAAGTTCCTGGTAAAATCTAATAGCTTAACTATAGTATGCTAGGAATACTGTTGTACTAGAGGGCGGGAGAGGTCTGAGGTACTTCAGGGGTAGGGGTGAAATCCTATAATCCTTGAAGGACCACCAGTGGCGAGGGCGTCAGACTGGAACGCGCCTGAAGTGAGGGACGAAAGCCAGGGGAGCGAACCGGATTAGATACCCGGTAGTCCTGGCCGTAAACGATGCACACTAGGTGTGGTATGGCTATTGAGCCCATATCAGTGCCGAAGGGAAACCCATTAAGCGTGCCGCCTGGGGAAGTACGGTCGCAAGGCTAAAACTAAAAGGAATTGGCGGGGGAGCACCACAAAGGGGTGAAGCCTGCGGTTCAATTGGACTCAACGCCGGGAAAACTTCCCAGGGGAGACAGCAGAAATGAAAAGTCAGGTTGACGACCTTACTTAACGAGCTGAGAGGAGGGTGCCATGGCCGTCGCCAGTTCGTGCCGTGAGGTATCCTGTTAAGTCAGGCAACGAACGAGACCCGTGCTTTTAGTTCCCAGCAAGACGTCACGACTTCGATGGGAACACTAAAAGGACCGCCATCGATAAGATGGAGGAAGGAGCGGGCCAAGGCAGGTCAGTATGCCCCGAAACCCCTGGGCCACACGCGGGCTGCAATGGTATGAACAATGGGCTGTAACTCCGAAAGGAGAAACCAATCCCGAAATCATATCTCAGTTGGGATTGTTGGCTGTAACTCGCTGACATGAACGTGGAAT
>1128285
GGATAACCTGCCCTTGGGTCTGGGATAACCCCGGGAAACTGGGGATAATATCGGATAACGCATATGTGCTGGAATGCTTTATGCGTAAAATGGATTCGTCCGCCCAAGGATGGGTCTGCGGCCTATCAGGTAGTAGTGGGTGTAATGTACCTACTAGCCAACAACGGGTACGGGTTGTGAGAGCAAGAGCCCGGAGATGGATTCTGAGACATGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTTACAATGCGGGAAACCGTGATAAGGGAACACCGAGTGCCAGCATCATATGCTGGCTGTCCAGATGTGTAAACTACATCTGTTAGCAAGGGCCGGGCAAGACCGGTGCCAGCCGCCGCGGTAACACCGGCGGCCCGAGTGGTGACCGTTATTATTGGGTCTAAAGGGTCCGTAGCCGGTTTGGTCAGTCCTCCGGGAAATCTGATAGCTTAACTGTTAGGCTTTCGGGGGATACTGCCAGGCTTGGAACCGGGAGAGGTAAGAGGTACTACAGGGGTAGGAGTGAAATCTTGTAATCCCTGTGAGACCACCTGTGGCGAAGGCGTCTTACCAGAACGGGTTCGACGGTGAGGGACGAAAGCTGGGGGCACGAACCGGATTAGATACCCGGGTAGTCCCAGCCGTAAACTATGCTCGCTAGGTGTCAGGCATGGCGCGACCGTGTCTGGTGCCGCAGGGAAGCCGTGAAGCGAGCCACCTGGGAAGTACGGCCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACAACAACGGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGACAACTCACCGGGGACGACAGCAATATGTAGGCCAGGCTGAAGACCTTGCCTGAATCGCTGAGAGGAGGTGCATGGCCGTCGCCAGTTCGTACTGTGAAGCATCCTGTTAAGTCAGGCAACGAGCGAGACCCGTGCCCACTGTTACCAGCATATCCTCCGGGATGATGGGTACTCTGTGGGGACCGCTGATGTTAAATCAGAGGAAGGTGCGGGCTACGGTAGGTCAGTATGCCCCGAATTTCCCGGGCTACACGCGGGCTACAATGAATGGGACAATGGGCCCCTACCCTGAAAAGGTTTGGTAATCTCACAAACCCATCCGTAGTTCGGATTGAGGGCTGTAACTCGCCCTCATGAAGCTGGAATCCGTAGTAATCGCGTTTCAATATAGCGCGGTGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCAAACCACCCGAGTGAGGTATGGGTAAGGGCACGAACTCTGTGTCGTGTTCGAACCTGTGCTTTGCAAGGGGGGTTAAGTCGTAACAAGGTAGCCGTAGGGGAATCTGCGGCTGGATCACCCCCT
>3770699
CGGTTGATCCTGCCGGTGGTCACTGCTATAAAATTTCGATTAAGACATGCTAGTTTAGATTTGTGTTTACATAGATCAGCGTACAGCTCAGTAATACATAATTAACATACTATCAGGTAGTGGATATCCTCGGGAAACTGAGGTTAATACACTATAATCATTAACTTCTGGAAAGATTCTATGATTAAAGCTTCGGCGCCTGATAATTGGATTATGCCTTATTAGGTCGTAGTGGGTGTAAAGGACCCCCTAGCCTACGATAAGTACGGGTCATGAGAGTGATAGCCCGGAGACGAATTCTGAGATAATAATTCGGTTACTACGGTATACCAGCAGTCGCGTAACATTCACAATGGGGGAAACCCTGATGATGGGAGTTTTAGTGCTACATTTGTAGCTGTATAGAAGTTTAAATAGCTTTTAGAGAAAGGACAGGGTAATACATGTGCCAGCCTCCGCGGTAAAACATGATGTCCAAGTGGTGATCGCTTTTATTGAGTCTAAAACGTTCGTAGCCTGTAAATTGTACCTATAGTGAAACCTACTTGCTTAACAAGTAGAATATTATAGCCATACGTTTACTAGAAATTGGATGAGGTTTGTGGTACTGCTTGGGTAGAGATAAAATCCGTTGATCCTTGCATGACCAGCGATGTAGCGAAGGCAACAAACCAATACAAATTTGACGGTCAGGAACGAAACCTAGGGTAGCAACGGGGATTAGATACCCCCTTAGTCCTAGGCGTAAACGCTGCTGACTAGATATTGGAAATTTTCAGTGTCCAAGCGAAGGCGATAAGTCAGCTACTTGAGGATTACGTCCGCAAGGATGAAACTTAAAGGAATTGGCGGGGGAGCACCGCAACGAGTGGAGCGTGCGGTTTAATTGAACCCAACGCCCGAAAACTTACCAAGAACCACTGAAAATATGAATGACAGTCTGAAGGGCTTTCTTGATTTCAGAAAGGTGGTGCATGGCCATCTCAAATTAATGCTGTGAAGTTTTCTATTAAGTTAGATAATTAATGAGATTTGCAACGTCTTTTGCTAGTCGAACTTTCGAGTTCGAAGATAAATGACGTGACTACCCGTGATAAAAAATGGGGGGAAGATGCAAGCTAAGGTAGGTCTGTATGCCCCGATGTTTCTTGGGCTACACGCGCGCTACAATGGACAAGACAACGAGTCGTGACATCGCAAGATGGAACTAATCTCTAAACTTGTTCGTAATTCGGATAGAAGTCTGTAACTCGGCTTCTTGAAGGTGGAATTCGTAGTAACTGTGGGTTAACATCCCGCGTTGAATATGCCACTGCTCCTTGCACACACCGCCCGTCAA
>3825327
AGGTGGCTGCTGTCGGGATGAGATTAAGTCATGCAACTGAGAGCACTACCTATGTATGTGCTCCGGGCAAGTCTGAGTAACGCGTAGTCAATCTACCCTGTGGTTGATGATAACCCCGGCAAACTGGGGATAAACGTCGATAATCACCGTCTGTTGGAATACTTCGGTGATAAAAGGAGTGTAAACATGGTTATACACGCCACAGGACGAGACTGCGTCTGATTAGGTATTGCGTGGGGTAATGGCCCACGTAGCCTTATCAGTAGGGGCTATGGGTAGTAGTATCCCCCAGTTGAATCCTGAGACACTGATTCAGGGCCTATGGGTTGCAGCAGGCACGAAAACTTCACAATGCACGAAAGTGTGATGAGGTCATCCCGAGTCCTAGGCTTACGTGGGGGGTTTTCTGGAGTGTGAAAAGCTTCAGGAATAAGGAGGGGGCAAGAACGGTGCCAGCCGCCGCGGTAAAACCGTCTCTTCGAGTGGCCACCGCGTTTACTGGGCTTAAAGCGTGCGTAGCGGGATTAGTCCGTCCCACATTAAAGACGGCTTCTTAAGGGTCCGAAATGTGTGGGAAACAGCTGATCTTGGCAATGGGATAGGGGCTCGGTACCCGTGGTGTAAAGGTGAAATTTTATAATCCCACGGGGACCACCGATGGCGAAGGCAGAGCCCTGGAACATGTGCGACCGTCAGGCACGAAAGGTGGTAGCAGCGGATAGATACTGTTAGATGATGATCAGCTGAAAACCCGGTAGTCCACCCCTAAACGATGCGGATTAAGTGTATGGGAAGCGTATGCTTTTCCATTTGCCGGTAGGGGAAACCGTTAAATTCCGCCGCCCTGGGAAGTATCGCTCTGCCAGAGTGAAACTTAAAAGCCAATTGGCGGGGAGAGGCGCCCACACATGGGTGGGAGGCCTGCGGGGTTTAATTTGAACTCAACGCCCGGGAAACTCACCCAGAAGTCTTTTTTTCCGATTGCCCAACCAGGCTTGAAGAAGCTTGTTGAAAAGGATTGAAAAGGGAAGTGGCATGGCCGTCTTTCCAGGCTCGTGCCCGTGGAGGTGTCCTTGTTAAGTCAGGCACCCCAGCCGAGATTCTCCCGGGGAATACTTTACCAGCCGGAACCCTAATCGGTTTGCCCGGGCACAAGTATTTCCCGACTGCCCACTGCTAAAGTGGAGGAAGGCCGGGAGGCCAAGGCAGGTCAGTATGCTCCCTAATACTCTGGGCCGCACGCGGGCTACAATGCTACGGACAACGGGATCCTACTCCGAAAGGCGACGGAAATCTCTAAACCGTAGCTCAGTTGGAATTGCGGGCTGCAACTGCCCGCATGAACTTGGAATCCATAGTAATCGTGTGTCATCATCGCACGGTGAATACTGTCCCCTCTCTTTGCACACACCGCCCGTCGCAGCACGCGAGATGGTCAAGTGAGAGGC
>801940
AATTCCCAATAGGTCAGTCAAGTTGGAATGCTGACTGATTTAAAACGTGCACATCATGTTGTGTAACGGCCTTTTGATGAGTCTGCGTCCGATTAGCTAGTAGGTGGGGTTATGGCCCACCTAGGCGAGGATCGGTAAGGGCAGTGAGAGCTGTAGCCCTAAGATGGCCACTGAGACAACGGGCCAGGCCCTACGGGGTGCAGCAGGTACGAAACCTCACCAATGCACGAAAGTGTGAGTGGGCTAACCTCAGTGCCAGGCGTCGTCCTGGCTTTTCCCAAGCGTACATAACTTGGGGAATAAGGAGAGGACAAGACTGGTGCCAGCCCCCGCGGTAAAACCAGCTCTTCGAATGGTAAGCATGATTATTGGGCCTAAAGCGTGCGTAGCCTGCTTGCAAGTCTCCAGATAAAGCTCACGTCTTAAGCGTGAAATCCCTGGGGATACTACAGGCCTTGGACTGGGACAGGGCGAGGGTACGTGTCCGGTAGGGGTGAATCCTATAATCGAACACGACCACCGGTGGCGAAGCGCCTCGCCTGGAACAGTCCGACGTGAGGCACGAAAGCCAGGGTAGCGAGCCGGATTAGATACCCGGGTAGTCCTGGCTGTAAACGATGCGGATTAGGTGTTGCGGTACACACGAAGTATCGCAGTGCCGAAGCGAAGGCGTTAAATCTGCCGCCTGGGAAGTACGCTCGCAAGGGTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAAGGGGTGGAGCGTGCGGTTTAATTGGACTCAACGCCGGAAAGCTTACCTGGGCAGACAGCATCATGATTGTCAGGTTGAAGGCCTTACATGAATAGCTGAGAGGAGGTGCATGGCCGTCGCCAGCTCGTGCCGTGATCCTCTAGCGTGGAGATCTATCATCGTTGCCAGAGGACGGTAAAGGTGTCCTGTTAAGTCAGGCAACGAGCGAGACCGGAGCCCTTAGTTGCCAGCGATAACTGCGGTTAGTCGGGTACACTAAGGGGACCGCCAGTGATGAAACTGGAGGAAGGATCCGTCCACGGCAGGTCAGTATGCCCCGATAGCTCAGGGCCACACGCGGGCTACAATGGCACGGACAATAGGTTCCGACATCGAAAGATGGAGGTAATCCCGAAACCGTGTCCCAGTTGGGATTGTGGGTTGGAACCCACCCACATGAACTTGGAATCCCTAGTAGTCGCATGTCATCATCGTGCGGCGAATACGTCCCTGCTCCTTGCACACACCGCCCGTCGCAGCATGCGAGGCGGGTTGGCCTGAGATGGCTGCTTTGTGTGGTCCTCGAGGGTTAATTCGCTGAGCAGGCTGAAGTCGTAACAAGGTAGCCGTA
>823009
TTCCGGTTGATCCTGCCGGAGGGTACTACTATTCGGATTCGACTAAGCCATGCGAGCCGAGAGTCTTCGGGACTCGGCATACTGCTCAGTAATATATAGTTAACCTACCCTAAAGTCAGGGATAATCTCGAGAAATTGAGGCTAATACCTGATATGTATTCTGGTCTGGAATGATAGAATATTTAAAGATCCGTCGCTTTAGGATGGGACTATACCTTATCAGTCTGTTGTGGGTGTAATGTACCCCCAAAACGATAACGAGTACGAGCCATGAGAGTGGAAGCTCGGAGATGGATTCTGAGACATGAATCCAGGTCCTACGGGACGCAGCAGGCGCGAAACCTTCACTATGTATTCACGTGCGATGAGGGAATCTGGAGTGCTTATGCTTAGCATAAGCTTTTTTCGAGTTTAAACAGCTTGGAGAATAAGGGGTGGGCAATACAAGTGCCAGCCGCCGCGGTAATACTTGAGCCCCAAGCGGTACCCAGTTTTAGTTGGTCTAAAGCGTCCGTAGCCGGTCTTGTTAGTCCTTAGTGAAATCTACTGGAAAACTGGTAGGCTTGCTGGGGATACTGCAAGACTTGGGACTGGGAGAGGGTAGATGTACTGCTAGGGAAGGGGTAAAATCCTATAATCCTAGTGGGACAACCTGTGGCGAAGGCGTCTACCTAGAACAGGTCCGACGGTGAGGGACGAAACCTAGGGGAGCGATCGGGATTAGATATGAGAAGGGAAGTTTTTATATAAAGTAAACCATAATATCTTCCTTTCTCACTAAATACCCCGGTAGTCCTAGGCGTAAACGATGCCCACTTGGTGTTACAAACCTTACGAGGGTTTGTAGTGCCGAAGCGTAGGTGTTAAGTGGGCCACCTGGGGAGTACGGCCGCAAGGTTGAAACTTAAGAGAATTGGCGGGGGAGCACACAAGGAGTGGAGGCTACGGTTCAATTGGATCCAACACCGGGAATCTTACGGGGATCGACAGCAGGATGAGGGTCAGTCTAAAGGGCTTACCAGACAAGCTGAGAAGTGTTGCATGGCCATCGTCAGCTCGTATCGTGAGACGTGCGGTCAAGTCCGTTAACGAGCGAGATCCGCATTCTATGTTGCTAACTCGCAAGAGTGCACTCATAGAAGACTGCTGGTGATAAATCAGAGGAAGGTGCGGGCGACGGTAGGTCAGTATGGCCTGAATTTCCCCGGCTACACGCGGCCTACAATGTACGAGACAGTGGGATGCAACCCTGAAAAGGGAAGCCAATCTCTTAACCTCGTACTCAGTACGGATCGAGGGTTGTAACTCACCCTCGTGAAGCTGGAATTCCTAGTAGGCAAACGTCATCATCGT
>4455990
GATGCTGGAATGCCCTGTAATCCAAAGTTCCGACGCCCTAGGATGGATCTGCGGCCGATTAGGTTGTTGTTGGGGTAATGGCCCAACAAGCCCGTAATCGGTACGGGTTGTGGGAGCAAGAGCCCGGAGTTGGATTCTGAGACACGAATCCAGGCCCTACGGGGCGCAGCAGGCGCGAAAACTTTACAATGCGGGCAACCGTGATAAGGGAACCTCGAGTGCCTGTAAATGCAGGCTGTTCAGGTGCCTAAAACACACCTGAATAAAGGGCCGGGCAAGACCGGTGCCAGCCGCCGTCGGTAATACCGGCGGCTCGAGTGGTGGCCGCTTTTATTGGGCTTAAAGCGTTCGTAGCTGGGTTGTTAAGTCTCTTGGGAAATCTGGCGTGCTTAACCGTCAGGCGTCTAACGGGATACTGGCAATCTTGGAACCTCGGCTCGAGTGGTGGCCGCTTTTATTGGGCTTAAAGCGTTCGTAGCTGGGTTGTTAAGTCTCTTGGGAAATCTGGCGGCTTAACCGTCAGGCGTCTAAGGGATACTGGCAATCTTGGAACCGGGAGAGGTGAGGGGTACTTCGGGGGTAGGAGTGAAATCCTGTAATCCTCGAGGGACCACCTGTGGCGAAGGCGCCTCACCAGAACGGCTTCGACAGTGAGGGACGAAAGCTGGGGGAGCAAACCGGATTAGATACCCGGGTAGTCCCAGCCGTAAACTATGCGCGTTAGGTGTATCGGTGACCACGAGTTACCGAGGTGCCGAAGGGAAACCGTGAAACGTGCCGCCTGGGAAGTACGGTCGCAAGGCTGAAACTTAAAGGAATTGGCGGGGGAGCACCACAACAGGTGGAGCCTGCGGTTTAATTGGACTCAACGCCGGGAAGCTCACCGGATAAGACAGCAGAATGATTGCCGGGCTGAAGACTCTGCATGACTAGCTGAGAGGAGGTGCATGGCCGTCGTCAGTTCGTACTGTGAAGCATCCTGTTAAGTCAGGCAACGAGCAAGACCCACGCCAACAGTTGCCAGCATGGTCTCCGGACTGATGGGGACACTGTTGGGACCGCCTCTGCTAAAGAGGAGGAAGGAATGGGCAACGGTAGGTCAGCATGCCCTGAATTATCCGGGCTACACGCGGGCTACAATGGGCAGGACAATGGGCATCGACACCGAAAGGTGAAGGCAATCTCCTAAACCTGTCCTTAGTTCGGATTGTGGGCTGCAACTCGCCCACATGAAGCTGGAATCTGTAGTAATCGCGTTTCAAAATAACGCGGTGAATTTGTCCCTGCTCCTTGCACACACCGCCCGTCAAACCACCCGAGTGGGGTTTGGATGAGGTTGCGGTTGTTGCCGCAGTCGAATCTAGGTTCCGCAAGGGGGGTTAAGTCGTAACAAGGTAGCCGTAGGGGAATCTGC
"""
taxonomies = """229854 k__Bacteria; p__Proteobacteria; c__Gammaproteobacteria; o__Legionellales; f__Legionellaceae; g__Legionella; s__
3761685 k__Bacteria; p__OD1; c__; o__; f__; g__; s__
3825327 k__Archaea; p__Crenarchaeota; c__MHVG; o__; f__; g__; s__
426860 k__Archaea; p__[Parvarchaeota]; c__[Parvarchaea]; o__YLA114; f__; g__; s__
4363563 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__
4336814 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__Pelagibacteraceae; g__; s__
823009 k__Archaea; p__Euryarchaeota; c__DSEG; o__ArcA07; f__; g__; s__
4423155 k__Bacteria; p__OP11; c__OP11-1; o__; f__; g__; s__
4455990 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanomicrobiales; f__Methanomicrobiaceae; g__Methanoculleus; s__bourgensis
801940 k__Archaea; p__Crenarchaeota; c__MHVG; o__; f__; g__; s__
4459468 k__Bacteria; p__Proteobacteria; c__Deltaproteobacteria; o__Desulfobacterales; f__Desulfobulbaceae; g__; s__
3779572 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Streptophyta; f__; g__; s__
4251079 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__
1128285 k__Archaea; p__Euryarchaeota; c__Methanomicrobia; o__Methanosarcinales; f__Methanosarcinaceae; g__Methanosarcina; s__
2107103 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__
3770699 k__Archaea; p__[Parvarchaeota]; c__[Parvarchaea]; o__WCHD3-30; f__; g__; s__
4391683 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Sphingomonadales; f__Sphingomonadaceae; g__; s__
4452949 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__
4363260 k__Bacteria; p__Cyanobacteria; c__Chloroplast; o__Chlorophyta; f__; g__; s__
3190878 k__Bacteria; p__Proteobacteria; c__Alphaproteobacteria; o__Rickettsiales; f__mitochondria; g__; s__
696036 k__Bacteria; p__Tenericutes; c__Mollicutes; o__Anaeroplasmatales; f__Anaeroplasmataceae; g__Asteroleplasma; s__
1928988 k__Archaea; p__Crenarchaeota; c__MBGB; o__; f__; g__; s__"""
t = {}
for e in taxonomies.split('\n'):
fields = e.split('\t')
t[fields[0]] = fields[1]
taxonomies = t
s = []
for seq_id, seq in parse_fasta(sequences.split('\n')):
s.append(DNA(seq[:250], '%s (%s)' % (seq_id, taxonomies[seq_id])))
sequences = SequenceCollection(s)
print len(sequences)
We can then compute k-word distances between the sequences.
In [2]:
def k_word_distance(s1, s2):
s1_k_words = set(s1.k_words(8))
s2_k_words = set(s2.k_words(8))
shared_k_words = s1_k_words & s2_k_words
return 1 - (len(shared_k_words) / max(len(s1_k_words), len(s2_k_words)))
In [3]:
k_word_distances = sequences.distances(k_word_distance)
Build a guide tree.
In [4]:
from scipy.cluster.hierarchy import average, dendrogram, to_tree
In [5]:
guide_lm = average(k_word_distances.condensed_form())
guide_d = dendrogram(guide_lm, labels=k_word_distances.ids, orientation='right',
link_color_func=lambda x: 'black')
In [6]:
from skbio import TreeNode
In [7]:
guide_tree = TreeNode.from_linkage_matrix(guide_lm, k_word_distances.ids)
And then do progressive alignment
In [8]:
from skbio.core.alignment.pairwise import global_pairwise_align_nucleotide
def progressive_msa(query_sequences, guide_tree, pairwise_aligner=global_pairwise_align_nucleotide):
# we need a parallel implementation of this functionality, and a Cython/C global aligner that can handle
# alignment of alignments. If done right, it could have a big impact on the field. Contact
# gregcaporaso@gmail.com if you have any interest in working on this.
c1, c2 = guide_tree.children
if c1.is_tip():
c1_aln = query_sequences[c1.name]
else:
c1_aln = progressive_msa(query_sequences, c1, pairwise_aligner)
if c2.is_tip():
c2_aln = query_sequences[c2.name]
else:
c2_aln = progressive_msa(query_sequences, c2, pairwise_aligner)
return pairwise_aligner(c1_aln, c2_aln)
In [9]:
msa = progressive_msa(sequences, guide_tree)
We can next build a tree from this multiple sequence alignment. To do that, we'll first compute the Hamming distances between the sequences, and then pass the resulting DistanceMatrix to the average function (for now this is a UPGMA tree, in the future, we'll update to use skbio's neighbor joining function).
In [10]:
from scipy.spatial.distance import hamming
msa_distances = msa.distances(hamming)
In [11]:
lm = average(msa_distances.condensed_form())
d = dendrogram(lm, labels=msa_distances.ids, orientation='right',
link_color_func=lambda x: 'black')
In [11]:
In [11]:
In [11]: