diff --git a/docs/content/gingr.rst b/docs/content/gingr.rst index b3c4147..c28deb6 100644 --- a/docs/content/gingr.rst +++ b/docs/content/gingr.rst @@ -1,3 +1,7 @@ +===== +Gingr +===== + .. image:: gingr/logo_med.png Gingr is an interactive tool for exploring large-scale phylogenies in tandem with their corresponding multi-alignments. Gingr can display informative overviews for hundreds or thousands of genomes, while allowing researchers to move quickly to more detailed views of specific subclades and genomic regions, even down to the nucleotide level of their multi-alignments. Additionally, its dynamic display of variants allows interactive selection of various filters, such as indels, poorly aligned regions and suspected sites of recombination. Gingr works chiefly in tandem with Parsnp, an efficient tool for core-genome multi-alignment and phylogenetic reconstruction. It is also applicable, however, to other analytical tools, accepting standard file formats such as multi-Fasta, XMFA, Newick and VCF. diff --git a/docs/content/gingr/quickstart.rst~ b/docs/content/gingr/quickstart.rst~ deleted file mode 100644 index 4f24904..0000000 --- a/docs/content/gingr/quickstart.rst~ +++ /dev/null @@ -1,37 +0,0 @@ -Quickstart -========== - -Browsing a Gingr file --------------------- -* Download [parsnp.ggr] -* Open in Gingr (File->Open) -* [ggr.png] -* The phylogeny appears on the left. Hover over a clade to highlight and outline the corresponding tracks to the right. -* [clade.png] -* Click to zoom in on the clade -* [zoomed.png] -* The multiple alignment appears on the right, shown as a SNP heatmap when zoomed out. To see the full alignment, zoom in with the mouse wheel or by selecting a region in the ruler. -* [bases.png] - -Importing other files ---------------------- -* Create a new workspace (File->New) -* [new.png] -* Download the data files - * Alignment: [parsnp.xmfa] - * Reference: [england1.fna] - * Annotations: [england1.gbk] - * Tree: [parsnp.tree] -* Import the alignment with the refrence (File->Import Alignment (XMFA & Fasta)) -* [xmfa.png] -* The track highlighted in blue ("england.gbk.fna.srt") is the current reference for variants. Select a new reference by right-clicking on a track. -* [reref.png] -* Next, import the phylogenetic tree (File->Import tree (Newick)) -* [tree.png] -* Reroot the tree at the midpoint (Tree->Reroot at midpoint) -* [reroot.png] -* The tree will now be balanced at the center of the longest path -* [rerooted.png] -* Finally, import the annotations (File->Import annotations (Genbank)) -* [annotated.png] -* The workspace can be saved to share or return to later (File->Save) diff --git a/docs/index.rst b/docs/index.rst index 7264337..83648f2 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -42,7 +42,7 @@ detection, and phylogenetic trees. Contents: .. toctree:: - :maxdepth: 5 + :maxdepth: 1 :numbered: content/hardware