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    :maxdepth: 2
 
    gingr/quickstart
+   gingr/types
    gingr/components
    gingr/installation
    gingr/paramaters
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+File formats
+============
+
+The flowchart below describes the various file formats that can be imported or
+exported to/from Gingr (or the `harvesttools` command line utility).
+
+.. image:: flowchart.png
+
+* Alignments
+	* Core only: The Gingr file format stores core alignments, or alignments that involve all genomes. When alignments are loaded, blocks that are not core will be discarded.
+	* Multi-fasta: This format does not store rearrangement information, so the alignment is treated as a single LCB.
+* References
+	* XMFA files can be accompanied by Fasta reference files to provide sequence between LCBs and to allow Genbank annotations (which must have matching GI numbers) to be loaded later. Genbank files that contain sequence can also be used as references.
+	* Multi-fasta alignments will use the first sequence as the reference. Genbank annotations can be loaded later if the GIs match.
+* Variants
+	* VCF files do not store complete alignment information, so any insertions larger than one base will be replaced by an LCB boundary. The first haplotype of each genotype is used to construct the multi-alignment, and subsequent haplotypes in diploid or polyploid genotypes will be ignored. While VCF can be output, it will be stripped down to essentially haploid genotypes, qualities, and filters.
+	* The multi-fasta SNP output is the same format as multi-fasta alignments, but only contains columns with variants (like a Mauve SNP file). This is useful for generating phylogenetic trees, but does not contain positional information or rearrangements.