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OPENSEQ.org
ntd p52_1_130
Genes: A B A+B
Length: 130 130 250
Sequences: 907 238 14
Seq/Len: 6.98 1.83 0.06
MirrorTree (Pazo et al. 2001) 0.62
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 0.51 0.02 0.02
2 0.56 0.02 0.02
5 0.58 0.02 0.02
10 0.58 0.02 0.02
20 0.59 0.02 0.02
100 0.59 0.02 0.03
∞ 0.60 0.02 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 (0.06 < 0.6).
 WARNING: The input alignment may be corrupted!
  • For sequence A, there is a high ratio (0.60 > 0.4) of paralogs.
ID Seq/Len Name Options I_Prob Status
2247 0.86 ntd p52_1_130 Δgene:(0, 0) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) 0.81 Done
2241 0.64 ntd p52_1_130 Δgene:(0, 0) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) 0.03 Done
2239 0.02 ntd p52_1_130 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-02, 8) msa: Jackhmmer (2015_03) Killed
2238 0.02 ntd p52_1_130 Δgene:(1, ∞) A:(1E-02, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) Killed
2237 0.06 ntd p52_1_130 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2015_03) Killed
2236 0.06 ntd p52_1_130 Δgene:(1, ∞) A:(1E-04, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) Killed
2235 0.09 ntd p52_1_130 Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: Jackhmmer (2015_03) Killed
2234 0.09 ntd p52_1_130 Δgene:(1, ∞) A:(1E-10, 8) B:(1E-10, 8) msa: Jackhmmer (2015_03) Killed
2233 0 ntd p52_1_130 Δgene:(0, 0) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
2232 0 ntd p52_1_130 Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
2227 0 ntd p52_1_130 Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2015_03) Killed - Shared
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