Skip to content

Commit

Permalink
fix table (biopython#4910)
Browse files Browse the repository at this point in the history 
Co-authored-by: Michiel Jan Laurens de Hoon <[email protected]>
  • Loading branch information
@mdehoon
mdehoon and Michiel Jan Laurens de Hoon authored Jan 15, 2025
1 parent 4a220bd commit 851a7a2
Showing 1 changed file with 94 additions and 95 deletions.
189 changes: 94 additions & 95 deletions Doc/Tutorial/chapter_align.rst
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1665,101 +1665,100 @@ formats can also be written by ``Bio.Align``, as shown in the table.

.. container:: center

+-------------+-------------+-------------+-------------+-------------+
| File format | Description | text / | Supported | Subsection |
| ``fmt`` | | binary | by | |
| | | | ``write`` | |
+-------------+-------------+-------------+-------------+-------------+
| ``a2m`` | A2M | text | yes | `1.7.11 |
| | | | | <#subsec:al |
| | | | | ign_a2m>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``bed`` | Browser | text | yes | `1.7.14 |
| | Extensible | | | <#subsec:al |
| | Data (BED) | | | ign_bed>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``bigbed`` | bigBed | binary | yes | `1.7.15 <#s |
| | | | | ubsec:align |
| | | | | _bigbed>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``bigmaf`` | bigMaf | binary | yes | `1.7.19 <#s |
| | | | | ubsec:align |
| | | | | _bigmaf>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``bigpsl`` | bigPsl | binary | yes | `1.7.17 <#s |
| | | | | ubsec:align |
| | | | | _bigpsl>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``chain`` | UCSC chain | text | yes | `1.7.20 <# |
| | file | | | subsec:alig |
| | | | | n_chain>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``clustal`` | ClustalW | text | yes | `1.7.2 <#su |
| | | | | bsec:align_ |
| | | | | clustal>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``emboss`` | EMBOSS | text | no | `1.7.5 <#s |
| | | | | ubsec:align |
| | | | | _emboss>`__ |
+-------------+-------------+-------------+-------------+-------------+
| `` | Exonerate | text | yes | `1 |
| exonerate`` | | | | .7.7 <#subs |
| | | | | ec:align_ex |
| | | | | onerate>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``fasta`` | Aligned | text | yes | `1.7.1 <# |
| | FASTA | | | subsec:alig |
| | | | | n_fasta>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``hhr`` | HH-suite | text | no | `1.7.10 |
| | output | | | <#subsec:al |
| | files | | | ign_hhr>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``maf`` | Multiple | text | yes | `1.7.18 |
| | Alignment | | | <#subsec:al |
| | Format | | | ign_maf>`__ |
| | (MAF) | | | |
+-------------+-------------+-------------+-------------+-------------+
| ``mauve`` | Mauve | text | yes | `1.7.12 <# |
| | eXtended | | | subsec:alig |
| | Multi-FastA | | | n_mauve>`__ |
| | (xmfa) | | | |
| | format | | | |
+-------------+-------------+-------------+-------------+-------------+
| ``msf`` | GCG | text | no | `1.7.6 |
| | Multiple | | | <#subsec:al |
| | Sequence | | | ign_msf>`__ |
| | Format | | | |
| | (MSF) | | | |
+-------------+-------------+-------------+-------------+-------------+
| ``nexus`` | NEXUS | text | yes | `1.7.8 <# |
| | | | | subsec:alig |
| | | | | n_nexus>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``phylip`` | PHYLIP | text | yes | `1.7.4 <#s |
| | output | | | ubsec:align |
| | files | | | _phylip>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``psl`` | Pattern | text | yes | `1.7.16 |
| | Space | | | <#subsec:al |
| | Layout | | | ign_psl>`__ |
| | (PSL) | | | |
+-------------+-------------+-------------+-------------+-------------+
| ``sam`` | Sequence | text | yes | `1.7.13 |
| | Al | | | <#subsec:al |
| | ignment/Map | | | ign_sam>`__ |
| | (SAM) | | | |
+-------------+-------------+-------------+-------------+-------------+
| `` | Stockholm | text | yes | `1 |
| stockholm`` | | | | .7.3 <#subs |
| | | | | ec:align_st |
| | | | | ockholm>`__ |
+-------------+-------------+-------------+-------------+-------------+
| ``tabular`` | Tabular | text | no | `1.7.9 <#su |
| | output from | | | bsec:align_ |
| | BLAST or | | | tabular>`__ |
| | FASTA | | | |
+-------------+-------------+-------------+-------------+-------------+
+---------------+-------------+-------------+-------------+-------------+
| File format | Description | text / | Supported | Subsection |
| ``fmt`` | | binary | by | |
| | | | ``write`` | |
+---------------+-------------+-------------+-------------+-------------+
| ``a2m`` | A2M | text | yes | `1.7.11 |
| | | | | <#subsec:al |
| | | | | ign_a2m>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``bed`` | Browser | text | yes | `1.7.14 |
| | Extensible | | | <#subsec:al |
| | Data (BED) | | | ign_bed>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``bigbed`` | bigBed | binary | yes | `1.7.15 <#s |
| | | | | ubsec:align |
| | | | | _bigbed>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``bigmaf`` | bigMaf | binary | yes | `1.7.19 <#s |
| | | | | ubsec:align |
| | | | | _bigmaf>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``bigpsl`` | bigPsl | binary | yes | `1.7.17 <#s |
| | | | | ubsec:align |
| | | | | _bigpsl>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``chain`` | UCSC chain | text | yes | `1.7.20 <# |
| | file | | | subsec:alig |
| | | | | n_chain>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``clustal`` | ClustalW | text | yes | `1.7.2 <#su |
| | | | | bsec:align_ |
| | | | | clustal>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``emboss`` | EMBOSS | text | no | `1.7.5 <#s |
| | | | | ubsec:align |
| | | | | _emboss>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``exonerate`` | Exonerate | text | yes | `1 |
| | | | | .7.7 <#subs |
| | | | | ec:align_ex |
| | | | | onerate>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``fasta`` | Aligned | text | yes | `1.7.1 <# |
| | FASTA | | | subsec:alig |
| | | | | n_fasta>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``hhr`` | HH-suite | text | no | `1.7.10 |
| | output | | | <#subsec:al |
| | files | | | ign_hhr>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``maf`` | Multiple | text | yes | `1.7.18 |
| | Alignment | | | <#subsec:al |
| | Format | | | ign_maf>`__ |
| | (MAF) | | | |
+---------------+-------------+-------------+-------------+-------------+
| ``mauve`` | Mauve | text | yes | `1.7.12 <# |
| | eXtended | | | subsec:alig |
| | Multi-FastA | | | n_mauve>`__ |
| | (xmfa) | | | |
| | format | | | |
+---------------+-------------+-------------+-------------+-------------+
| ``msf`` | GCG | text | no | `1.7.6 |
| | Multiple | | | <#subsec:al |
| | Sequence | | | ign_msf>`__ |
| | Format | | | |
| | (MSF) | | | |
+---------------+-------------+-------------+-------------+-------------+
| ``nexus`` | NEXUS | text | yes | `1.7.8 <# |
| | | | | subsec:alig |
| | | | | n_nexus>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``phylip`` | PHYLIP | text | yes | `1.7.4 <#s |
| | output | | | ubsec:align |
| | files | | | _phylip>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``psl`` | Pattern | text | yes | `1.7.16 |
| | Space | | | <#subsec:al |
| | Layout | | | ign_psl>`__ |
| | (PSL) | | | |
+---------------+-------------+-------------+-------------+-------------+
| ``sam`` | Sequence | text | yes | `1.7.13 |
| | Alignment/ | | | <#subsec:al |
| | Map (SAM) | | | ign_sam>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``stockholm`` | Stockholm | text | yes | `1 |
| | | | | .7.3 <#subs |
| | | | | ec:align_st |
| | | | | ockholm>`__ |
+---------------+-------------+-------------+-------------+-------------+
| ``tabular`` | Tabular | text | no | `1.7.9 <#su |
| | output from | | | bsec:align_ |
| | BLAST or | | | tabular>`__ |
| | FASTA | | | |
+---------------+-------------+-------------+-------------+-------------+

.. _`subsec:align_fasta`:

Expand Down

0 comments on commit 851a7a2

Please sign in to comment.