Archive for April, 2008

Notes on Deception Butte, OR

April 26, 2008

Deception Butte, Oregon, Willamette National Forest
Mileage: maybe 7 miles round trip?
Elevation gain: 2500 feet
On 04/26/2008, the roundtrip hike took 4 hours.

Obscure notes for the future:

1. The trailhead can be hard to find. . .

The map says: the trail starts on the north side of Deception Creek.

I say: the trailhead is actually on the south side of the creek.  It looks like the trail was recently re-routed.  Here are updated directions: coming from Eugene on Highway 58, drive over the Deception Creek bridge, past the Deception Creek trailer park, and turn right onto Deception Creek road. Drive about 50 yards to the trailhead, which looks like this:

2. The first mile follows the river; its easy and groovy. After crossing a wooden bridge at the river fork, the trail starts seriously climbing. Parts were super slippery with snow and mud; I regret not bring trekking poles.

3. The summit is densely forested and the views are anticlimactic. For better views with less work, check-out Mount June.

These noise machines. . .

April 18, 2008

. . . need tuning, but making noise is so much fun.

MP3 file (8.8 MB): piano

MP3 file (1.7 MB): guitar and such

A counterexample of elision’s efficacy over culling.

April 2, 2008

In response to “Elision: A Method for Accommodating Multiple Molecular Sequence Alignments with Alignment-Ambiguous Sites” Wheeler et al. 1995:

In most cases, elision is useful for resolving alignment-ambiguous sites in a multiple sequence alignment (MSA).  Although Wheeler et al. show that elision is better at resolving MSA ambiguities than culling, here is one counterexample in which elision and culling perform equally:

Consider two putative MSAs (as shown in the figure below). In MSA #1, taxa A and B are more homologous than taxa C. In MSA #2, taxa B and C are more homologous than taxa A. The image below illustrates this case, using a three-character alphabet {gamma, delta, epsilon}. MSA #1 and MSA #2 produce symmetrically opposite phylogenies. When we cull over these MSAs, we produce a star tree (because we cull-out both columns 1 and 2). Furthermore, when we elide over these MSAs we also produce a star tree. Consequently, in this example elision and culling both produce equal support for B = “gamma indel” and B = “indel gamma”.


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