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Edge lengths were computed using the standard OLS because WLS and GLS can potentially lead to inconsistent results et al. [ 45].
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A filtered design variable with a minimum length is computed using a Helmholtz-type differential equation.
Spines were then traced manually and the spine head width or the spine length was computed using the SimplePCI software with the experimenter blinded to the condition.
All the lengths of stay were computed using exact days (number of hours/24) but for cases missing any information on time, we calculated lengths of stay according to the rule proposed by Ruttiman and Pollack [ 33].
For 454 data (where the problem of multimatching reads is mitigated or simply eliminated, because of reads' lengths) transcription levels were computed using in house Bash and Perl scripts to parse Blast or Bowtie outputs.
Branch lengths for the tree were computed using PAML (fix_blength = 0).
The branch lengths of these phylogenies were computed using an exponential distribution.
Growth indices of length-for-age z-score (LAZ), weight-for-age z-score (WAZ), and weight-for-length z-scores (WLZ) were computed using WHO Anthro software (http://www.who.int/childgrowth/software/en/).
Based on the coordinates and the calibration of body length, the following parameters were computed using the same program.
The search parameters used in this analysis are being compared to the default search parameters used in the TRF program in the Additional file 1. TR characteristics such as the density and mean length of repeat types were computed using the program Sat-Stat, version 1.3.1 developed by CM.
Nutritional status indices (Z-scores for length-for-age [LAZ], weight-for-length [WLZ], weight-for-age [WAZ]) were computed using World Health Organisation (WHO) 2005 Child Growth Standards in the ANTHRO Software v3.0.1 (ANTHRO, WHO, Geneva).
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