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OPENSEQ.org
cI_L_M
Genes: A B A+B
Length: 613 509 1047
Sequences: 12096 16403 10
Seq/Len: 19.73 32.23 0.01
MirrorTree (Pazo et al. 2001) 0.92
Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.

[Show Jackhmmer results] - Maybe useful in deciding what regions to trim.
Δgene Ratio of paralogs Joined
A B Seq/Len
1 0.39 0.52 0.01
2 0.43 0.57 0.01
5 0.59 0.71 0.02
10 0.60 0.71 0.02
20 0.60 0.72 0.02
100 0.60 0.72 0.02
∞ 0.60 0.72 0.02
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 (0.01 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence B, there is a high ratio (0.52 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
2377 1 cI_B_C Δgene:(1, ∞) A:(1E-60, 1) B:(1E-60, 1) msa: Jackhmmer (2015_03) 0.95 Done - Shared
2263 0.01 cI_L_M Δgene:(1, 1) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) Killed - Shared
2262 10.81 cI_L_M Δgene:(0, 0) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) 1.00 Done - Shared
2261 0.02 cI_L_M Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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