Release associated with manuscript in Applications in Plant Sciences. -- Added paralog_investigator.py, which detects and extracts long exons from putative paralogs in all genes in one sample. -- Added paralog_retriever.py, which retrieves sequences generated by paralog_investigator.py for many samples (or the coding sequence generated by exonerate_hits.py if no paralogs are detected). -- Added a test_dataset of 13 genes for 9 samples, and a shell script to run the test data through the main script and several post-processing scripts. -- Fixed bug involving calling HybPiper with a relative path such as: ../reads_first.py -- reads_first.py --check_depend now checks for SPAdes, BWA, and Samtools -- Full revision of README, which is now shorter. Full tutorials on installing and running HybPiper are now on the Wiki.