GY180307: Updated README

README.md

@@ -14,7 +14,7 @@ cuti file.csv -d, -n pvalue > pvalues
 
 [**`cons`**](cons): intelligent consensus formation
 
-`cons` aims to solve problems deriving accurate consensus data from alignments with uneven depths across their length. This is a frequent problem with alignments of sequences clustered by [`vsearch`](https://github.com/torognes/vsearch), [`usearch`](http://www.drive5.com/usearch/), or [`cd-hit-est`](http://weizhongli-lab.org/cd-hit/). Intuitively, a small region of low depth within a larger region of higher depth is of comparatively less relevance than if the same low depth formed a larger, indepentent, region at a different position within the alignment. Normal methods using thresholding approaches will either remove all or include all of these regions, if the threshold is high or low, respectively. `cons` run with `-l/--local` treats the alignment as a time series, and performs changepoint detection to determine localised regions of equivalent depth. These are smoothed (`-s/--smooth`) to remove small regions present due to indels, for example, and a consensus is derived using thresholds appropriate for each region independently.
+`cons` aims to solve problems deriving accurate consensus data from alignments with uneven depths across their length. This is a frequent problem with alignments of sequences clustered by [`vsearch`](https://github.com/torognes/vsearch), [`usearch`](http://www.drive5.com/usearch/), or [`cd-hit-est`](http://weizhongli-lab.org/cd-hit/). Intuitively, a small region of low depth within a larger region of higher depth is of comparatively less relevance than if the same low depth formed a larger, independent, region at a different position within the alignment. Normal methods using thresholding approaches will either remove all or include all of these regions, if the threshold is high or low, respectively. `cons` run with `-l/--local` treats the alignment as a time series, and performs changepoint detection to determine localised regions of equivalent depth. These are smoothed (`-s/--smooth`) to remove small regions present due to indels, for example, and a consensus is derived using thresholds appropriate for each region independently.
 ```bash
 cons [-h] -n NAME [-a [AMBIG]] [-m [MIN]] [-g [GLOB]] [-l [LOCAL]]
     [-s [SMOOTH]] [-w] [--retaingaps] [--changepoints] [input]