Add README for haploid case

README.md

@@ -1,2 +1,19 @@
 # lshmm
-code to run Li and Stephens
+This is a Python library for prototyping and testing implementations of algorithms using the Li & Stephens (2003) HMM.
+
+## Usage
+
+### Inputs
+Reference panel contains sample and/or (partial) ancestral haplotypes.
+
+### Demo
+Forwards algorithm
+Backwards algorithm
+Viterbi algorithm
+Log-likelihood evaluation of a copying path
+
+### Features
+* Scaling of mutation rate by the number of distinct alleles per site.
+* Non-copiable allelic state in the reference panel (`NONCOPY`).
+* Missing allelic state in the query (`MISSING`).
+* Multiallelic sites.