|
| Genes: |
A |
B |
A+B |
| Length: |
77 |
128 |
203 |
| Sequences: |
260 |
1312 |
16 |
| Seq/Len: |
3.38 |
10.25 |
0.08 |
| MirrorTree (Pazo et al. 2001) |
0.96 |
|
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Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
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Jackhmmer results
Sequence A: (Date: 2016_06b) 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: 2016_06b) 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 Jackhmmer 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 |
| 5316 |
19.24 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 2) B:(1E-20, 2) msa: Jackhmmer (2016_06b)
|
0.02 |
Done - Shared |
| 5315 |
10.12 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 1) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 5314 |
1.32 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 2) msa: Jackhmmer (2016_06b)
|
0.06 |
Done - Shared |
| 5312 |
0.15 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 2) B:(1E-40, 8) msa: Jackhmmer (2016_06b)
|
|
Killed - Shared |
| 5311 |
0 |
Vi-Vc |
Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 4) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 5309 |
35.47 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 4) B:(1E-20, 2) msa: Jackhmmer (2016_06b)
|
0.00 |
Done - Shared |
| 5308 |
0.08 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 1) B:(1E-40, 8) msa: Jackhmmer (2016_06b)
|
|
Killed - Shared |
| 5307 |
0 |
Vi-Vc |
Δgene:(1, 1) A:(1E-40, 4) B:(1E-40, 2) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 5301 |
0 |
Vi-Vc |
Δgene:(1, 1) A:(1E-60, 8) B:(1E-60, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 5300 |
0.17 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 8) msa: Jackhmmer (2016_06b)
|
|
Killed - Shared |
| 5298 |
0 |
Vi-Vc |
Δgene:(1, 1) A:(1E-60, 4) B:(1E-60, 4) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 5297 |
0.07 |
Vi-Vc |
Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b)
|
|
Killed - Shared |
| 5289 |
22.37 |
Vi-Vc |
Δgene:(1, 1) A:(1E-10, 4) B:(1E-40, 4) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 5288 |
22.35 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 4) B:(1E-40, 4) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 5286 |
26.12 |
Vi-Vc |
Δgene:(1, 1) A:(1E-04, 8) B:(1E-04, 8) msa: Jackhmmer (2016_06b)
|
0.00 |
Done - Shared |
| 5285 |
22.35 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 4) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 5272 |
26.53 |
Vi-Vc |
Δgene:(1, 1) A:(1E-10, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b)
|
0.00 |
Done - Shared |
| 5271 |
73.84 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 5259 |
22.35 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 5258 |
25.07 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 8) B:(1E-20, 8) msa: Jackhmmer (2016_06b)
|
0.01 |
Done - Shared |
| 5257 |
0.17 |
Vi-Vc |
Δgene:(1, 1) A:(1E-20, 8) B:(1E-40, 8) msa: Jackhmmer (2016_06b)
|
|
Killed - Shared |