that one configuration, which they called "standard", was the most common throughout all the studied areas. Remarkably, they also noticed that four different strains could be obtained from the standard sequence by a single inversion, and two others could be related by a second inversion. This allowed them to hypothesize a phylogeny for the sequences, and to infer that the standard sequence was probably also the ancestral one. Linguistic Evolution Reconstructions of the words and phenomes of ancient proto-languages such as Proto-Indo-European have been performed based on the observed analogues in present-day languages. Typically, these analyses are carried out manually using the "comparative method". First, words from different languages with a common etymology (cognates) are identified in the contemporary languages under study, analogous to the identification of orthologous biological sequences. Second, correspondences between individual sounds in the cognates are identified, a step similar to biological sequence alignment, although performed manually. Finally, likely ancestral sounds are hypothesised by manual inspection and various heuristics (such as the fact that most languages have both nasal and non-nasal vowels). Software There are many software packages available which can perform ancestral state reconstruction. Generally, these software packages have been developed and maintained through the efforts of scientists in related fields and released under free software licenses. The following table is not meant to be a comprehensive itemization of all available packages, but provides a representative sample of the extensive variety of packages that implement methods of ancestral reconstruction with different strengths and features. Package descriptions Molecular evolution The majority of these software packages are designed for analyzing genetic sequence data. For example, PAML is a collection of programs for the phylogenetic analysis of DNA and protein sequence alignments by maximum likelihood. Ancestral reconstruction can be performed using the codeml program. In addition, LAZARUS is a collection of Python scripts that wrap the ancestral reconstruction functions of PAML for batch processing and greater ease-of-use. Software packages such as MEGA, HyPhy, and Mesquite also perform phylogenetic analysis of sequence data, but are designed to be more modular and customizable. HyPhy implements a joint maximum likelihood method of ancestral sequence reconstruction that can be readily adapted to reconstructing a more generalized range of discrete ancestral character states such as geographic locations by specifying a customized model in its batch language. Mesquite provides ancestral state reconstruction methods for both discrete and continuous characters using both maximum parsimony and maximum