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OPENSEQ.org
V2
Genes: A B A+B
Length: 593 458 1026
Sequences: 897 5280 48
Seq/Len: 1.51 11.53 0.05
MirrorTree (Pazo et al. 2001) 0.97
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 0.07 0.14 0.04
2 0.07 0.43 0.04
5 0.07 0.44 0.05
10 0.07 0.45 0.05
20 0.07 0.46 0.05
100 0.07 0.47 0.05
∞ 0.09 0.51 0.05
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 (0.05 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.46 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
12243 0.05 V Δgene:(1, 20) A:(1E-40, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed
12242 0.05 V Δgene:(1, 20) A:(1E-20, 8) B:(1E-80, 8) msa: HHblits (2015_06) Killed
12240 0.05 V Δgene:(1, 20) A:(1E-20, 8) B:(1E-60, 8) msa: HHblits (2015_06) Killed
12237 0.05 V5 Δgene:(1, 20) A:(1E-80, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
12236 0.05 V4 Δgene:(1, 20) A:(1E-02, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
12235 0.05 V3 Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed
12234 0.05 V2 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: HHblits (2015_06) Killed - Shared
12233 0.05 V Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Killed - Shared
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