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OPENSEQ.org
Test_4
Genes: A B A+B
Length: 221 171 392
Sequences: 37 3150 12
Seq/Len: 0.17 18.42 0.03
MirrorTree (Pazo et al. 2001) 0.10
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 0.01 0.08 0.00
2 0.01 0.08 0.00
5 0.01 0.08 0.00
10 0.01 0.08 0.00
20 0.01 0.08 0.00
100 0.01 0.08 0.01
∞ 0.01 0.09 0.03
Paired alignment generation
None of the genomes have hits within 20 Δgene.
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 (0.03 < 0.6).
ID Seq/Len Name Options I_Prob Status
13416 0 Reta Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
7474 0.04 Test_20_jack Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed
7473 0 Test_10_jack Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) Killed
7472 0 Test_4_jack Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed
7471 0.03 Test_4 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed
7470 0.03 Test_10 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed
7469 0.03 Test_20 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
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