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OPENSEQ.org
DK
Genes: A B A+B
Length: 492 523 1015
Sequences: 2537 2129 1
Seq/Len: 5.16 4.07 0
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 0.61 0.56 0.00
2 0.62 0.58 0.00
5 0.63 0.59 0.00
10 0.65 0.59 0.00
20 0.65 0.60 0.00
100 0.75 0.71 0.00
∞ 0.76 0.74 0.00
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 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.65 > 0.4) of paralogs.
  • For sequence B, there is a high ratio (0.60 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
4432 0.26 DK Δgene:(1, 20) A:(1E-04, 2) B:(1E-04, 2) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4431 0.5 DK Δgene:(1, 20) A:(1E-10, 1) B:(1E-10, 1) msa: Jackhmmer (2015_06) 0.00 Done - Shared
4430 0 DK Δgene:(1, 20) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_06) Killed - Shared
4429 0 DK Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_06) Killed - Shared
3662 0.48 DK Δgene:(1, 20) A:(1E-20, 1) B:(1E-20, 1) msa: Jackhmmer (2015_06) 0.01 Done - Shared
3617 0 DK Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_06) Killed - Shared
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