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.
NOTE: for the sake of runtime, I'm currently computing the alignment from only the first slice_length bases of the sequences. This results in our final tree being pretty terrible in this example. For a better tree (and longer run time) increase the value of the slice_length variable.
In [1]:
import collections
import io
import skbio.io
from skbio import DNA
slice_length = 100
display_tax_levels = 2
fasta = io.StringIO(""">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 = io.StringIO("""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:
fields = e.rstrip('\n').split('\t')
t[fields[0]] = fields[1]
taxonomies = t
sequences = collections.OrderedDict()
for seq in skbio.io.read(fasta, format='fasta'):
seq_id = seq.metadata['id']
seq_tax = ' '.join(taxonomies[seq.metadata['id']].split('; ')[:display_tax_levels])
seq_id = '%s (%s)' % (seq.metadata['id'], seq_tax)
sequences[seq_id] = DNA(sequence=seq[:slice_length], metadata={'id': seq_id})
print(len(sequences))
In [2]:
next(iter(sequences.values()))
Out[2]:
We can then compute kmers distances between the sequences.
In [3]:
import functools
from skbio.sequence.distance import kmer_distance
from skbio import DistanceMatrix
kmer_distances = DistanceMatrix.from_iterable(sequences.values(), metric=functools.partial(kmer_distance, k=8), key='id')
Build a guide tree.
In [4]:
from scipy.cluster.hierarchy import average, dendrogram, to_tree
%matplotlib inline
In [5]:
guide_lm = average(kmer_distances.condensed_form())
guide_d = dendrogram(guide_lm, labels=kmer_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, kmer_distances.ids)
And then do progressive alignment
In [8]:
from skbio.alignment 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
# [email protected] 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)[0]
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 skbio.sequence.distance import hamming
msa_distances = DistanceMatrix.from_iterable(msa, metric=hamming, key='id')
In [11]:
lm = average(msa_distances.condensed_form())
d = dendrogram(lm, labels=msa_distances.ids, orientation='right',
link_color_func=lambda x: 'black')
