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OPENSEQ.org
K1-Tb
Genes: A B A+B
Length: 333 418 746
Sequences: 3770 1040 73
Seq/Len: 11.32 2.49 0.1
MirrorTree (Pazo et al. 2001) 0.30
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show HHblits results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.02 0.06 0.01
2 0.03 0.06 0.01
5 0.04 0.06 0.03
10 0.05 0.07 0.05
20 0.07 0.07 0.10
100 0.14 0.10 0.28
∞ 0.24 0.18 0.56
Paired alignment generation
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Sequence A E-value:
Iterations:
Sequence B E-value:
Iterations:
Δgene MSA
Figure 1: The effect of Δgene on ratio of paralogs in the genome for each gene, and the number of sequences in the resulting joined alignment. Figure 2: Distribution of Δgene across all genomes. Figure 3: Current parameters. You can use the form to adjust the parameters and resubmit the job!
GREMLIN results
  • ERROR: Not enough sequences to run GREMLIN analysis on (0.1 < 0.6).
ID Seq/Len Name Options I_Prob Status
1291 0.29 K1-Tb Δgene:(1, 100) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) 0.00 Done - Shared
1289 0.1 K1-Tb Δgene:(1, 20) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1287 0.1 K1-Tb Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2013_03) Killed - Shared
1285 0.1 K1-Tb Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2013_03) Killed - Shared
1283 0.09 K1-Tb Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2013_03) Killed - Shared
1281 0.11 K1-Tb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2014_03) Killed - Shared
1277 0.1 K1-Tb Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2013_03) Killed - Shared
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