Links in README to other software

README.md

@@ -14,15 +14,15 @@ To hopefully answer the question, "Can I use polyRAD?":
 
 polyRAD requires as input the sequence read depth at each allele for each sample.  Alleles must also be grouped into loci.  The bioinformatics pipeline that you used for SNP discovery did not have to assume polyploidy, as long as it faithfully reported allelic read depth.  Genomic alignment information is optional.  Right now there are data import functions for the following formats:
 
-* Variant Call Format (VCF).  The allele depth (AD) genotype field must be present.  I have tested the import function on files produced by the TASSEL GBSv2 pipeline.  It should also work for GATK.
-* TagDigger.  This is another piece of software I created, which reads FASTQ files and expected tag sequences and outputs a CSV file with read counts at samples x tags.
-* UNEAK.  The UNEAK pipeline outputs read depth in a file called HapMap.hmc.txt, which can be read by polyRAD.  (Beware that read depth is capped at 127 by UNEAK; TagDigger can help you if you expect high depth to be common in your dataset.)
-* Stacks version 1.  If you have catalog files (catalog.alleles.tsv etc.) and matches files (matches.tsv) generated by Stacks, they can be imported by polyRAD.
+* [Variant Call Format (VCF)](https://samtools.github.io/hts-specs/).  The allele depth (AD) genotype field must be present.  I have tested the import function on files produced by the [TASSEL GBSv2](https://bitbucket.org/tasseladmin/tassel-5-source/wiki/Tassel5GBSv2Pipeline) pipeline.  It should also work for [GATK](https://software.broadinstitute.org/gatk/).
+* [TagDigger](https://github.com/lvclark/tagdigger).  This is another piece of software I created, which reads FASTQ files and expected tag sequences and outputs a CSV file with read counts at samples x tags.
+* [UNEAK](https://tassel.bitbucket.io/TasselArchived.html).  The UNEAK pipeline outputs read depth in a file called HapMap.hmc.txt, which can be read by polyRAD.  (Beware that read depth is capped at 127 by UNEAK; TagDigger can help you if you expect high depth to be common in your dataset.)
+* [Stacks version 1](http://catchenlab.life.illinois.edu/stacks/).  If you have catalog files (catalog.alleles.tsv etc.) and matches files (matches.tsv) generated by Stacks, they can be imported by polyRAD.
 
 Currently there are export functions for the following software.  Genotypes are exported as continuous rather than discrete variables.
 
-* GAPIT
-* rrBLUP
+* [GAPIT](http://www.zzlab.net/GAPIT/)
+* [rrBLUP](https://cran.r-project.org/web/packages/rrBLUP/)
 
 ## Installation