|
| Genes: |
A |
B |
A+B |
| Length: |
400 |
350 |
657 |
| Sequences: |
718 |
3475 |
709 |
| Seq/Len: |
1.79 |
9.93 |
1.08 |
| MirrorTree (Pazo et al. 2001) |
0.98 |
|
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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 |
| 11266 |
0.7 |
Mce4A-Mce4B |
Δgene:(1, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 11265 |
0.7 |
Mce4A-Mce4B |
Δgene:(1, 2) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 11264 |
0.7 |
Mce4A-Mce4B |
Δgene:(1, 5) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 11263 |
0.01 |
Mce4A-Mce4B |
Δgene:(1, 20) A:(1E-40, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 11262 |
0 |
Mce4A-Mce4B |
Δgene:(1, 20) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 11253 |
0.71 |
Mce4A-Mce4B |
Δgene:(1, 20) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 11244 |
1.08 |
Mce4A-Mce4B-2 |
Δgene:(0, 2) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06)
|
1.00 |
Done - Shared |
| 11243 |
1.08 |
Mce4A-Mce4B-2 |
Δgene:(0, 1) A:(1E-02, 8) B:(1E-04, 8) msa: HHblits (2015_06)
|
1.00 |
Done - Shared |
| 11242 |
1.08 |
Mce4A-Mce4B-2 |
Δgene:(0, 1) A:(1E-02, 2) B:(1E-04, 2) msa: HHblits (2015_06)
|
1.00 |
Done - Shared |
| 11241 |
0.7 |
Mce4A-Mce4B |
Δgene:(1, 10) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 11233 |
0.7 |
Katherine |
Δgene:(0, 1) A:(1E-40, 8) B:(1E-40, 8) msa: HHblits (2015_06)
|
0.00 |
Done - Shared |
| 11232 |
0 |
Mce4A-Mce4B |
Δgene:(1, 1) A:(1E-80, 8) B:(1E-80, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 11231 |
1.08 |
Mce4A-Mce4B-2 |
Δgene:(0, 1) A:(1E-02, 2) B:(1E-02, 2) msa: HHblits (2015_06)
|
1.00 |
Done - Shared |
| 11230 |
0.01 |
Mce4A-Mce4Bx3 |
Δgene:(1, 1) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06)
|
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Killed - Shared |
| 11229 |
0.01 |
Mce4A-Mce4B-2 |
Δgene:(1, 100) A:(1E-02, 8) B:(1E-02, 8) msa: HHblits (2015_06)
|
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Killed - Shared |
| 11223 |
0.02 |
Katherine |
Δgene:(1, 20) A:(1E-04, 8) B:(1E-04, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |
| 11214 |
0.03 |
Mce4A-Mce4B |
Δgene:(1, 20) A:(1E-20, 8) B:(1E-20, 8) msa: HHblits (2015_06)
|
|
Killed - Shared |