The Aligner plug-in has an improved algorithm and will perfectly align both the phase and polarities of two (or more) mono or stereo audio signals easily and quickly.
Any recording engineer has probably experienced problems with multi-microphone recordings that, when mixing together, can sound weak and "phasey." Of course you may fix these problems manually in a time consuming process of visually sliding individual tracks ahead or behind in time. Sometimes the differences are initially imperceptible.
I tried Aligner on 15 recorded drum tracks of a drum kit that I did not record that sounded okay, but was terribly phasey and not at all mono-compatible.
Nugen Audio's Aligner measures time differences in samples between a selected reference track and the track(s) under scrutiny. I chose the kick drum mic (track) as my reference. Since each mic (track) is a different physical distance from the kick drum mic, they were all various low numbers of samples late in time. You can bypass all Aligner plug-ins all at once or only individual channels.
In the case of this first class-sounding drum recording, the difference with/without Aligner running was very slight but noticeable. The sound was fatter, more full range and you can use as many Aligner instances as you require.
I experimented with bypassing different channels and using a different channel as reference. Aligner features two kinds of bypass controls: one for all tracks at once and another for each individual channel. You can flip polarity and manually change the amount of delay.
I also aligned a distant room mic with a reference for a guitar sound. The room mic had a coloration I liked, but its delay times/distances were detrimental—Aligner captured the color and pulled that room mic closer in time.
Nugen Audio Aligner ver 184.108.40.206 (as tested in Pro Tools Ultimate) sells for $49 MSRP.