I was newly married in 2016 and my wife has children of her own. should we file together or should she file on her own

[xmasbaby0 · Accepted solution]

If you were married at the end of 2016 your filing choices are married filing jointly or married filing separately.

Married Filing Jointly is usually better, even if one spouse had little or no income. When you file a joint return, you and your spouse will each receive the $4050 personal exemption, plus the married filing jointly standard deduction of $12,600 (add $1250 for each spouse over the age of 65).  You are eligible for more credits including education credits, earned income credit, child and dependent care credit, and a larger income limit to receive the child tax credit. 

If you choose to file married filing separately, both spouses have to file the same way—either you both itemize or you both use standard deduction. Your tax rate will be higher than on a joint return. Some of the special rules for filing separately include: you cannot get earned income credit, education credits, or deductions for student loan interest. A higher percent of your Social Security benefits may be taxable.  In many cases you will not be able to take the child and dependent care credit.  If you live in a community property state, you will be required to provide additional information regarding your spouse’s income.  If you are using online TurboTax to prepare your returns, you will need to prepare two separate returns and pay twice

[jerry2000]

Each year you can choose to file as Married Filing Separately. However, that may not provide the benefit that you expect, and you will almost always end up paying more in tax than if you file jointly.
The Married Filing Separately filing status is very different than the Single filing status. There are a number of severe restrictions on deductions and credits, and on the amount of IRA contributions that you can deduct, especially if you live together with your spouse.
You can not take the EIC,
You can not take the credit for Child and Dependent Care, in most cases,
You can not take the Education credits/deductions, and there are many other restrictions.
 If either of you receive Social Security benefits and you live with your spouse, more of the SS benefit will be taxable, and the person receiving it will have to include the SS benefit in their gross income when determining whether they have to file. If one of you itemizes deductions, the other must also itemize even if they have nothing to itemize.

Before you decide, you should carefully read the restrictions that go with MFS in  IRS Pub. 501, at this link:
http://www.irs.gov/pub/irs-pdf/p501.pdf

You should carefully read the limits on IRA deductions in IRS Pub. 590-A at this link:
http://www.irs.gov/pub/irs-pdf/p590a.pdf

In addition, if you live in a Community Property state, there are special rules you must follow for reporting income and expense. For further information on that, see IRS Pub. 555, at this link:
http://www.irs.gov/pub/irs-pdf/p555.pdf

and/or the Turbotax FAQ at this link:
https://ttlc.intuit.com/questions/1901162-married-filing-separately-in-community-property-states