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OPENSEQ.org
PopB - PopD
Genes: A B A+B
Length: 390 295 684
Sequences: 25 24 21
Seq/Len: 0.06 0.08 0.03
MirrorTree (Pazo et al. 2001) 0.92
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 0.02 0.02 0.03
2 0.02 0.02 0.03
5 0.02 0.02 0.03
10 0.02 0.02 0.03
20 0.02 0.02 0.03
100 0.02 0.02 0.03
∞ 0.02 0.02 0.03
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 (0.03 < 0.6).
ID Seq/Len Name Options I_Prob Status
14348 0.03 PopD_PopB Δgene:(1, 20) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
14345 translocon Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06) Running
9186 0.03 PopB - PopD Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06) Killed - Shared
9178 0.03 PopB - PopD Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06) Killed - Shared
9159 0.05 PopB - PopD Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132) Killed - Shared
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