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The possible functional effect of the single nucleotide variations (SNVs) was assessed using the PolyPhen-2 v1.3.5 software.

Since "software" is a noncount noun, and "v1.3.5" clearly indicates a specific version, it is okay to use "software" here, or it would be better to use "program"?

The possible functional effect of the single nucleotide variations (SNVs) was assessed using the PolyPhen-2 v1.3.5 program.

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    In any case, program sounds better. Though I share your concerns, I think the first sentence should have a piece of before software. – MadWard Jun 28 '16 at 7:32
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    Why you didn't say: software PolyPhen-2 v1.3.5. However, if the software is well-known, I think, you can omit the software and simply say: PolyPhen-2 v1.3.5 – Cardinal Jun 28 '16 at 7:37
  • other possible variants: PolyPhen-2 v1.3.5 package/utility/suite, whetever applies to the sofware best. – tum_ Jun 28 '16 at 10:25
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Sometimes a version number might be considered part of the name of the software, and in that case, one would not use the definite article or a noun after the proper noun.

Windows 2.0 is a crowd-pleaser.

unidiomatic The Windows 2.0 is a crowd-pleaser.
marginal The Windows 2.0 O/S is a crowd-pleaser.
unidiomatic Windows 2.0 O/S is a crowd-pleaser.

A version with subversion is not really the software's name but a sort of post-positioned determiner, and so we would not use the definite article with the version/subversion:

unidiomatic... using the PolyPhen-2 v1.3.5 software.

idiomatic spoken English:

... using PolyPhen version 1 dot 3 dot 5.

... using version 1.3.5 of the PolyPhen software.

... using version 1.3.5 of PolyPhen

But how one writes this may fall under the jurisdiction of the house style sheet.

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I've read it shifting the words:

The possible functional effect of the single nucleotide variations (SNVs) was assessed using the software PolyPhen-2 v1.3.5.

(please notice that I'm not a native English speaker)

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