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OPENSEQ.org
rfa 1 and rfa 2
Genes: A B A+B
Length: 621 273 837
Sequences: 502 487 49
Seq/Len: 0.81 1.78 0.06
MirrorTree (Pazo et al. 2001) 0.74
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 0.03 0.03 0.00
2 0.03 0.03 0.00
5 0.03 0.03 0.00
10 0.03 0.03 0.00
20 0.03 0.03 0.00
100 0.03 0.03 0.01
∞ 0.03 0.03 0.05
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 (0.06 < 0.6).
ID Seq/Len Name Options I_Prob Status
10212 0.06 rfa 1 and rfa 2 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06) Killed - Shared
10210 0.06 rfa 1 and rfa 2 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
10209 0.05 rfa 1 and rfa 2 Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
10203 0 rfa 1 and rfa 2 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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