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| Genes: |
A |
B |
A+B |
| Length: |
458 |
348 |
739 |
| Sequences: |
1886 |
1769 |
112 |
| Seq/Len: |
4.12 |
5.08 |
0.15 |
| MirrorTree (Pazo et al. 2001) |
0.68 |
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Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
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HHblits results
Sequence A: (Date: 2015_06) BEFORE and AFTER the coverage filter was applied, to remove sequences that don't cover at least 75% of query length. Regions above red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len.
Sequence B: (Date: 2015_06) BEFORE and AFTER the coverage filter was applied, to remove sequences that don't cover at least 75% of query length. Regions above red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len.
[Show HHblits results] - Maybe useful in deciding what regions to trim. |
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| 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! |
| ID |
Seq/Len |
Name |
Options |
I_Prob |
Status |
| 10335 |
0.05 |
RadA-RecA2 |
Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 10334 |
0.09 |
RadA-RecA2 |
Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (r132)
|
0.00 |
Done - Shared |
| 10332 |
2.14 |
RadA-RecA2 |
Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (r132)
|
0.01 |
Done - Shared |
| 10330 |
1.28 |
RadA-RecA2 |
Δgene:(1, ∞) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.23 |
Done - Shared |
| 10329 |
0.05 |
RadA-RecA2 |
Δgene:(1, 20) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 10325 |
0.15 |
RadA-RecA2 |
Δgene:(1, 100) A:(1E-06, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.02 |
Done - Shared |
| 10324 |
1.29 |
RadA-RecA2 |
Δgene:(1, ∞) A:(1E-06, 8) B:(1E-80, 8) msa: HHblits (2015_06)
|
0.32 |
Done - Shared |
| 10321 |
1.29 |
RadA-RecA2 |
Δgene:(1, ∞) A:(1E-06, 8) B:(1E-06, 8) msa: HHblits (2015_06)
|
0.10 |
Done - Shared |
| 10310 |
1.29 |
RadA-RecA2 |
Δgene:(1, ∞) A:(1E-06, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
0.34 |
Done - Shared |
| 10309 |
1.29 |
RadA-RecA |
Δgene:(1, ∞) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
0.06 |
Done - Shared |
| 10303 |
2.14 |
infinite-E-80-Jack |
Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: Jackhmmer (r132)
|
0.01 |
Done - Shared |
| 10302 |
1.28 |
infinite-E-80-HHblist |
Δgene:(1, ∞) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06)
|
0.11 |
Done - Shared |
| 10301 |
1.29 |
infinite-E-60-HHblist |
Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06)
|
0.06 |
Done - Shared |
| 10300 |
2.14 |
infinite- E-60 |
Δgene:(1, ∞) A:(1E-60, 8) B:(1E-60, 8) msa: Jackhmmer (r132)
|
0.01 |
Done - Shared |
| 10298 |
0.2 |
RadA-RecA-interr |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (r132)
|
0.00 |
Done - Shared |
| 10297 |
0.05 |
RadA-RecA-interr |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |