Incorporate dnoise and pseudogene screening

[kbseah]

• Add option use DnoisE for entropy-based denoising and testing of different alpha and cluster size values (resolves issue #7)
• Add option to filter out likely pseudogenes by stop codons and screening of translation with an HMM, using pytransaln (resolves issue #11)
• Hard-code options in vsearch that user should not change (--sizein --sizeout) instead of exposing them in config file
• Rewrite config file to make keys more semantic, instead of exposing program-dependent options; gives us option of adding alternatives to current dependencies (e.g. a different trimming tool instead of cutadapt) - still in progress

Other issues are being worked on...

[kbseah]

• Calculate Faith's PD (resolves issue #5 )

[kbseah]

• Use table of samples and read files, resolves issue #10