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OPENSEQ.org
Ska2 and Ska3
Genes: A B A+B
Length: 121 101 205
Sequences: 5292 3740 30
Seq/Len: 43.74 37.03 0.15
MirrorTree (Pazo et al. 2001) 0.66
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 0.14 0.07 0.03
2 0.14 0.07 0.04
5 0.14 0.07 0.05
10 0.14 0.07 0.09
20 0.14 0.08 0.14
100 0.14 0.08 0.31
∞ 0.16 0.09 0.81
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 (0.15 < 0.6).
ID Seq/Len Name Options I_Prob Status
9910 0 Ska2 and Ska3 Δgene:(1, 2) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9906 0.15 Ska2 and Ska3 Δgene:(1, 20) A:(1E-04, 8) B:(1E-02, 8) msa: Jackhmmer (r132) Killed - Shared
9905 0.05 Ska2 and Ska3 Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (r132) Killed - Shared
9904 0 Ska2 and Ska3 Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (r132) Killed - Shared
9903 0 Ska2 and Ska3 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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