Question: Are gene sequences used to reconstruct baterial phylogeny?
About the article "Bacteria", section "Origin and early evolution".

Candidate passages:
The fact that genes can move between distant branches of the tree of life even at low probabilities raises challenges to scientists trying to reconstruct evolution by studying genes and gene sequences in different organisms.
Horizontal gene transfer (HGT) effectively scrambles the information on which biologists rely to reconstruct the phylogeny of organisms.
Furthermore, HGT poses challenges for the ambitious reconstruction of the earliest events in evolution.
Because the early branches of the tree of life spanned long time intervals and involved large numbers of organisms, many low-probability HGT events are certain to have occurred. 
Perfect phylogeny is a theoretical framework that can also be used in more practical methods.
One such example is that of Incomplete Directed Perfect Phylogeny.
This concept involves utilizing perfect phylogenies with real, and therefore incomplete and imperfect, datasets.
Such a method utilizes SINEs to determine evolutionary similarity.
These Short Interspersed Elements are present across many genomes and can be identified by their flanking sequences.
SINEs provide information on the inheritance of certain traits across different species.
Unfortunately, if a SINE is missing it is difficult to know whether those SINEs were present prior to the deletion.
By utilizing algorithms derived from perfect phylogeny data we are able to attempt to reconstruct a phylogenetic tree in spite of these limitations.
Perfect phylogeny is also used in the construction of haplotype maps.
By utilizing the concepts and algorithms described in perfect phylogeny one can determine information regarding missing and unavailable haplotype data.
By assuming that the set of haplotypes that result from genotype mapping corresponds and adheres to the concept of perfect phylogeny (as well as other assumptions such as perfect Mendelian inheritance and the fact that there is only one mutation per SNP), one is able to infer missing haplotype data.  
Phylogenetics may be applied to cells in tumors to reveal the evolutionary relationships between cells, just as it is used to reveal evolutionary relationships between organisms and species.
Shibata, Tavare and colleagues have exploited this to estimate the time between the initiation of a tumor and its detection in the clinic.
Louhelainen "et al."
have used parsimony to reconstruct the relationships between biopsy samples based on loss of heterozygosity.
Phylogenetic trees should not be confused with oncogenetic trees, which represent the common sequences of genetic events during neoplastic progression and do not represent the relationships of common ancestry that are essential to a phylogeny.
For an up-to-date review in this field, see Bast 2012  
The gene that encodes the CFTR protein is found on the human chromosome 7, on the long arm at position q31.2.
from base pair 116,907,253 to base pair 117,095,955.
CFTR orthologs have also been identified in all mammals for which complete genome data are available.
The "CFTR" gene has been used in animals as a nuclear DNA phylogenetic marker.
Large genomic sequences of this gene have been used to explore the phylogeny of the major groups of mammals, and confirmed the grouping of placental orders into four major clades: Xenarthra, Afrotheria, Laurasiatheria, and Euarchonta plus Glires. 
Bacteria were at first classified based solely on their shape (vibrio, bacillus, coccus etc.
), presence of endospores, gram stain, aerobic conditions and motility.
This system changed with the study of metabolic phenotypes, where metabolic characteristics were used.
Recently, with the advent of molecular phylogeny, several genes are used to identify species, the most important of which is the 16S rRNA gene, followed by 23S, ITS region, gyrB and others to confirm a better resolution.
The quickest way to identify to match an isolated strain to a species or genus today is done by amplifying it's 16S gene with universal primers and sequence the 1.4kb amplicon and submit it to a specialised web-based identification database, namely either Ribosomal Database Projectwhich align the sequence to other 16S sequences using infernal, a secondary structure bases global alignment, or ARB SILVA, which aligns sequences via SINA (SILVA incremental aligner), which does a local alignment of a seed and extends it [http://www.arb-silva.de/documentation/background/.
Several identification methods exists:  Phenotypic analyses * fatty acid analyses * Growth conditions (Agar plate, Biolog multiwell plates)  Genetic analyses * DNA-DNA hybridization * DNA profiling * Sequence * GC ratios  Phylogenetic analyses * 16S-based phylogeny * phylogeny based on other genes * Multi-gene sequence analysis * Whole-genome sequence based analysis